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 organi...
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doaj-781e94dc5186416ca650bc7db49a133b2020-11-25T02:31:30ZengSociedade Brasileira de GenéticaGenetics and Molecular Biology1678-468539466567310.1590/1678-4685-gmb-2015-0164S1415-47572016000400665Evolutionary analysis of apolipoprotein E by Maximum Likelihood and complex network methodsLeandro de Jesus BenevidesDaniel Santana de CarvalhoRoberto Fernandes Silva AndradeGilberto Cafezeiro BomfimFlora Maria de Campos FernandesAbstract 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.http://www.scielo.br/scielo.php?script=sci_arttext&pid=S1415-47572016000400665&lng=en&tlng=enApolipoprotein Ephylogenycomplex networkMaximum Likelihood |
collection |
DOAJ |
language |
English |
format |
Article |
sources |
DOAJ |
author |
Leandro de Jesus Benevides Daniel Santana de Carvalho Roberto Fernandes Silva Andrade Gilberto Cafezeiro Bomfim Flora Maria de Campos Fernandes |
spellingShingle |
Leandro de Jesus Benevides Daniel Santana de Carvalho Roberto Fernandes Silva Andrade Gilberto Cafezeiro Bomfim Flora Maria de Campos Fernandes Evolutionary analysis of apolipoprotein E by Maximum Likelihood and complex network methods Genetics and Molecular Biology Apolipoprotein E phylogeny complex network Maximum Likelihood |
author_facet |
Leandro de Jesus Benevides Daniel Santana de Carvalho Roberto Fernandes Silva Andrade Gilberto Cafezeiro Bomfim Flora Maria de Campos Fernandes |
author_sort |
Leandro de Jesus Benevides |
title |
Evolutionary analysis of apolipoprotein E by Maximum Likelihood and complex network methods |
title_short |
Evolutionary analysis of apolipoprotein E by Maximum Likelihood and complex network methods |
title_full |
Evolutionary analysis of apolipoprotein E by Maximum Likelihood and complex network methods |
title_fullStr |
Evolutionary analysis of apolipoprotein E by Maximum Likelihood and complex network methods |
title_full_unstemmed |
Evolutionary analysis of apolipoprotein E by Maximum Likelihood and complex network methods |
title_sort |
evolutionary analysis of apolipoprotein e by maximum likelihood and complex network methods |
publisher |
Sociedade Brasileira de Genética |
series |
Genetics and Molecular Biology |
issn |
1678-4685 |
description |
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. |
topic |
Apolipoprotein E phylogeny complex network Maximum Likelihood |
url |
http://www.scielo.br/scielo.php?script=sci_arttext&pid=S1415-47572016000400665&lng=en&tlng=en |
work_keys_str_mv |
AT leandrodejesusbenevides evolutionaryanalysisofapolipoproteinebymaximumlikelihoodandcomplexnetworkmethods AT danielsantanadecarvalho evolutionaryanalysisofapolipoproteinebymaximumlikelihoodandcomplexnetworkmethods AT robertofernandessilvaandrade evolutionaryanalysisofapolipoproteinebymaximumlikelihoodandcomplexnetworkmethods AT gilbertocafezeirobomfim evolutionaryanalysisofapolipoproteinebymaximumlikelihoodandcomplexnetworkmethods AT floramariadecamposfernandes evolutionaryanalysisofapolipoproteinebymaximumlikelihoodandcomplexnetworkmethods |
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