Referee report. For: Major histocompatibility complex (MHC) fragment numbers alone – in Atlantic cod and in general - do not represent functional variability [version 1; referees: 1 approved with reservations]

Anthony B. Wilson
2018
This correspondence concerns a publication by Malmstrøm in Nature et al. Genetics in October 2016. Malmstrøm made an important contribution et al. to fish phylogeny research by using low-coverage genome sequencing for comparison of 66 teleost (modern bony) fish species, with 64 of those 66 belonging to the species-rich clade Neoteleostei, and with 27 of those 64 belonging to the order Gadiformes. For these 66 species, Malmstrøm et al. estimated numbers of genes belonging to the major
more » ... he major histocompatibility complex (MHC) class I lineages U and Z and concluded that in teleost fish these combined numbers are positively associated with, and a driving factor of, the rates of establishment of new fish species (speciation rates). They also claimed that functional genes for the MHC class II system molecules MHC IIA, MHC IIB, CD4 and CD74 were lost in early Gadiformes. Our main criticisms are (1) that the authors did not provide sufficient evidence for presence or absence of intact functional MHC class I or MHC class II system genes, (2) that they did not discuss that an MHC subpopulation gene number alone is a very incomplete measure of MHC variance, and (3) that the MHC system is more likely to reduce speciation rates than to enhance them. We conclude that their new model of MHC class I evolution, reflected in their title "Evolution of the immune system influences speciation rates in teleost fish", is unsubstantiated. In addition, we explain that their "pinpointing" of the functional loss of the MHC class II system and all the important MHC class II system genes to the onset of Gadiformes is preliminary, because they did not sufficiently investigate the species at the clade border. Dijkstra JM and Grimholt U. How to cite this article: Major histocompatibility complex (MHC) fragment numbers alone -in Atlantic cod and in general -do not represent functional variability [version 1; peer review: 2 approved, 1 approved with reservations] F1000Research 2018, :963 ( ) 7 https://doi.Supplementary Table S1: Examples of sequence reads of major histocompatibility complex (MHC) class II system genes found in single read archive (SRA) datasets published by Malmstrøm et al. for Gadiformes and closely related fishes. Click here to access the data. Supplementary File 1: List of sequence reads in SRA datasets of Gadiformes published by Malmstrøm et al. that match with major histocompatibility complex (MHC) class II system genes. Click here to access the data. PubMed Abstract | Publisher Full Text 2. Borghans J, Keşmir C, de Boer RJ: MHC diversity in Individuals and Populations. In: Flower D, Timmis J, editors. In Silico Immunology. Springer, New York NY; 2007; 177-195. Publisher Full Text 3. Nei M, Rooney AP: Concerted and birth-and-death evolution of multigene families. Annu Rev Genet. 2005; 39: 121-52. PubMed Abstract | Publisher Full Text | Free Full Text 4. Grimholt U, Tsukamoto K, Azuma T, et al.: A comprehensive analysis of teleost MHC class I sequences. BMC Evol Biol. 2015; 15: 32. PubMed Abstract | Publisher Full Text | Free Full Text 5. Malmstrøm M, Jentoft S, Gregers TF, et al.: Unraveling the evolution of the Atlantic cod's (Gadus morhua L.) alternative immune strategy. PLoS One. 2013; 8(9): e74004. PubMed Abstract | Publisher Full Text | Free Full Text 6. Nonaka MI, Aizawa K, Mitani H, et al.: Retained orthologous relationships of the MHC Class I genes during euteleost evolution. Mol Biol Evol. 2011; 28(11): 3099-112. PubMed Abstract | Publisher Full Text 7. Miller KM, Li S, Ming TJ, et al.: The salmonid MHC class I: more ancient loci uncovered. Immunogenetics. 2006; 58(7): 571-89. PubMed Abstract | Publisher Full Text 8. Schümann J, Pittoni P, Tonti E, et al.: Targeted expression of human CD1d in transgenic mice reveals independent roles for thymocytes and thymic APCs in positive and negative selection of Valpha14i NKT cells. J Immunol. 2005; 175(11): 7303-10. PubMed Abstract | Publisher Full Text 9. Klein J, Sato A, Nikolaidis N: MHC, TSP, and the origin of species: from immunogenetics to evolutionary genetics. Annu Rev Genet. 2007; 41: 281-304. PubMed Abstract | Publisher Full Text 10. Doxiadis GG, de Groot N, Otting N, et al.: Haplotype diversity generated by ancient recombination-like events in the MHC of Indian rhesus macaques. Immunogenetics. 2013; 65(8): 569-84. PubMed Abstract | Publisher Full Text | Free Full Text
doi:10.5256/f1000research.16766.r35833 fatcat:uertzyoohvc2xhz3rcre7i6kky