Evolutionary analysis of apolipoprotein E by Maximum Likelihood and complex network methods

Abstract

Apolipoprotein E (apo E) is a human glycoprotein with 299 amino acids, and it is a major component of very low density lipoproteins (VLDL) and a group of high-density lipoproteins (HDL). Phylogenetic studies are important to clarify how various apo E proteins are related in groups of organisms and whether they evolved from a common ancestor. Here, we aimed at performing a phylogenetic study on apo E carrying organisms. We employed a classical and robust method, such as Maximum Likelihood (ML), and compared the results using a more recent approach based on complex networks. Thirty-two apo E amino acid sequences were downloaded from NCBI. A clear separation could be observed among three major groups: mammals, fish and amphibians. The results obtained from ML method, as well as from the constructed networks showed two different groups: one with mammals only (C1) and another with fish (C2), and a single node with the single sequence available for an amphibian. The accordance in results from the different methods shows that the complex networks approach is effective in phylogenetic studies. Furthermore, our results revealed the conservation of apo E among animal groups.

Comparison of complex networks and tree-based methods of phylogenetic analysis and proposal of a bootstrap method

“…Data of four enzymes present in the chitin metabolic pathway for 1695 organisms (with complete genomes) were collected and used to test and validate the method. This framework was also successfully applied to investigate the evolutionary origins of mitochondria using three ATP synthase subunits and its alphaproteobacterial homologs ( Carvalho et al, 2015 ), and to present an evolutionary study of apolipoprotein-E carrying organisms ( Benevides et al, 2016 ). Despite these advances, with large databases, we understand this approach should be widely tested, using distinct databases and taxonomic groups, and comparing its results with those provided the current methods quoted above.…”