About: Discovery of All Three Types in Cartilaginous Fishes Enables Phylogenetic Resolution of the Origins and Evolution of Interferons

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About: Discovery of All Three Types in Cartilaginous Fishes Enables Phylogenetic Resolution of the Origins and Evolution of Interferons Goto Sponge NotDistinct Permalink

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type	Academic Article research paper schema:ScholarlyArticle
isDefinedBy	Covid-on-the-Web dataset
title	Discovery of All Three Types in Cartilaginous Fishes Enables Phylogenetic Resolution of the Origins and Evolution of Interferons
Creator	Secombes, Christopher Zou, Jun Dooley, Helen Macqueen, Daniel Redmond, Anthony Ak, Redmond Buckley, Katherine Grayfer, Leon
source	PMC
abstract	Interferons orchestrate host antiviral responses in jawed vertebrates. They are categorized into three classes; IFN1 and IFN3 are the primary antiviral cytokine lineages, while IFN2 responds to a broader variety of pathogens. The evolutionary relationships within and between these three classes have proven difficult to resolve. Here, we reassess interferon evolution, considering key phylogenetic pitfalls including taxon sampling, alignment quality, model adequacy, and outgroup choice. We reveal that cartilaginous fishes, and hence the jawed vertebrate ancestor, possess(ed) orthologs of all three interferon classes. We show that IFN3 groups sister to IFN1, resolve the origins of the human IFN3 lineages, and find that intronless IFN3s emerged at least three times. IFN2 genes are highly conserved, except for IFN-γ-rel, which we confirm resulted from a teleost-specific duplication. Our analyses show that IFN1 phylogeny is highly sensitive to phylogenetic error. By accounting for this, we describe a new backbone IFN1 phylogeny that implies several IFN1 genes existed in the jawed vertebrate ancestor. One of these is represented by the intronless IFN1s of tetrapods, including mammalian-like repertoires of reptile IFN1s and a subset of amphibian IFN1s, in addition to newly-identified intron-containing shark IFN1 genes. IFN-f, previously only found in teleosts, likely represents another ancestral jawed vertebrate IFN1 family member, suggesting the current classification of fish IFN1s into two groups based on the number of cysteines may need revision. The providence of the remaining fish IFN1s and the coelacanth IFN1s proved difficult to resolve, but they may also be ancestral jawed vertebrate IFN1 lineages. Finally, a large group of amphibian-specific IFN1s falls sister to all other IFN1s and was likely also present in the jawed vertebrate ancestor. Our results verify that intronless IFN1s have evolved multiple times in amphibians and indicate that no one-to-one orthology exists between mammal and reptile IFN1s. Our data also imply that diversification of the multiple IFN1s present in the jawed vertebrate ancestor has occurred through a rapid birth-death process, consistent with functional maintenance over a 450-million-year host-pathogen arms race. In summary, this study reveals a new model of interferon evolution important to our understanding of jawed vertebrate antiviral immunity.
has issue date	2019-07-12(xsd:dateTime)
bibo:doi	10.3389/fimmu.2019.01558
bibo:pmid	31354716
has license	cc-by
sha1sum (hex)	0c76b6ad3636678e30cdb1093360aa425ba71928
schema:url	https://doi.org/10.3389/fimmu.2019.01558
resource representing a document's title	Discovery of All Three Types in Cartilaginous Fishes Enables Phylogenetic Resolution of the Origins and Evolution of Interferons
has PubMed Central identifier	PMC6640115
has PubMed identifier	31354716
schema:publication	Front Immunol
resource representing a document's body	covid:0c76b6ad3636678e30cdb1093360aa425ba71928#body_text
is schema:about of	named entity 'jawed vertebrate' named entity 'Origins' named entity 'HOST' named entity 'EVOLUTION' named entity 'IMPORTANT' named entity 'MILLION' named entity 'BIRTH' named entity 'OUR' named entity 'RAPID' named entity 'arms race' named entity 'reveals' named entity 'birth-death process' named entity 'evolution' named entity 'IL-10 family' named entity 'substitution model' named entity 'amphibian' named entity 'amniote' named entity 'TBLASTN' named entity 'IFN-γ' named entity 'catshark' named entity 'intronless' named entity 'evolution' named entity 'amniote' named entity 'jawed vertebrates' named entity 'α-helical' named entity 'phylogeny' named entity 'amniote' named entity 'class II' named entity 'morphology' named entity 'cysteine' named entity 'mycobacteria' named entity 'taxon sampling' named entity 'teleost' named entity 'gene' named entity 'Phyre2' named entity 'teleost' named entity 'interferons' named entity 'Interferons' named entity 'clades' named entity 'topology' named entity 'orthologous' named entity 'IFN' named entity 'amniote' named entity 'teleosts' named entity 'chicken' named entity 'taxon sampling' named entity 'Yule' named entity 'phylogeny' named entity 'cartilaginous fishes' named entity 'interferon' named entity 'paralogous' named entity 'evolutionary relationships' named entity 'lognormal' named entity 'phylogenies' named entity 'IFN' named entity 'coelacanth' named entity 'IFN-γ' named entity 'molecular clock' named entity 'viral pathogens' named entity 'vertebrate' named entity 'disulphide bridge' named entity 'orthology' named entity 'phylogenetic analyses' named entity 'teleosts' named entity 'posterior probability' named entity 'cartilaginous fishes' named entity 'peptide' named entity 'amphibians' named entity 'outgroup' named entity 'clade' named entity 'phylogenetic analyses' named entity 'reptile' named entity 'interferons' named entity 'orthologous'

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