De novo genotyping of the major histocompatibility complex in an Australian dragon lizard, Ctenophorus decresii

References

• Babik, W., Taberlet, P., Ejsmond, M., & Radwan, J. (2009). New generation sequencers as a tool for genotyping of highly polymorphic multilocus MHC system. Molecular Ecology Resources, 9, 713–719.
   PubMed Web of Science ®Google Scholar
• Bi, K., Vanderpool, D., Singhal, S., Linderoth, T., Moritz, C., & Good, J. M. (2012). Transcriptome-based exon capture enables highly cost-effective comparative genomic data collection at moderate evolutionary scales. BMC Genomics, 13(1), 403.
   PubMedGoogle Scholar
• Biedrzycka, A., Sebastian, A., Migalska, M., Westerdahl, H., & Radwan, J. (2016). Testing genotyping strategies for ultra-deep sequencing of a co-amplifying gene family: MHC class I in a passerine bird. Molecular Ecology Resources, 17(4), 642–655.
   PubMed Web of Science ®Google Scholar
• Bontrop, R. E., Otting, N., de Groot, N. G., & Doxiadis, G. G. M. (1999). Major histocompatibility complex class II polymorphisms in primates. Immunological Reviews, 167(1), 339–350.
   PubMedGoogle Scholar
• De Groot, N., Blokhuis, J. H., Otting, N., Doxiadis, G. G., & Bontrop, R. E. (2015). Co-evolution of the MHC class I and KIR gene families in rhesus macaques: Ancestry and plasticity. Immunological Reviews, 267(2015), 228–245.
   PubMedGoogle Scholar
• Delport, W., Poon, A. F., Frost, S. D., & Kosakovsky Pond, S. L. (2010). Datamonkey 2010: A suite of phylogenetic analysis tools for evolutionary biology. Bioinformatics, 26(19), 2455–2457.
   PubMed Web of Science ®Google Scholar
• Dirscherl, H., McConnell, S., Yoder, J., & Jong, J. (2014). The MHC class I genes of zebrafish. Developmental & Comparative Immunology, 46(1), 11–23.
   PubMed Web of Science ®Google Scholar
• Elbers, J., & Taylor, S. (2016). Major histocompatibility complex polymorphism in reptile conservation. Herpetological Conservation and Biology, 11(1), 1–12.
   Web of Science ®Google Scholar
• Ferrandiz-Rovira, M., Bigot, T., Allaine, D., Callait-Cardinal, M. P., & Cohas, A. (2015). Large-scale genotyping of highly polymorphic loci by next-generation sequencing: How to overcome the challenges to reliably genotype individuals. Heredity, 114(5), 485–493.
   PubMed Web of Science ®Google Scholar
• Gaigher, A., Burri, R., Gharib, W., Taberlet, P., Roulin, A., & Fumagalli, L. (2016). Family-assisted inference of the genetic architecture of major histocompatibility complex variation. Molecular Ecology Resources, 16(6), 1353–1364.
   PubMed Web of Science ®Google Scholar
• Galan, M., Guivier, E., Caraux, G., Charbonnel, N., & Cosson, J. (2010). A 454 multiplex sequencing method for rapid and reliable genotyping of highly polymorphic genes in large-scale studies. BMC Genomics, 11(296), 1–15.
   PubMedGoogle Scholar
• Garcia-Boronat, M., Diez-Rivero, C. M., Reinherz, E. L., & Reche, P. A. (2008). PVS: A web server for protein sequence variability analysis tuned to facilitate conserved epitope discovery. Nucleic Acids Research, 36, 35–41.
   PubMed Web of Science ®Google Scholar
• Glaberman, S., & Caccone, A. (2008). Species-specific evolution of class I MHC genes in iguanas (order: Squamata; subfamily: Iguaninae). Immunogenetics, 60(7), 371–382.
   PubMed Web of Science ®Google Scholar
• Glaberman, S., Du Pasquier, L., & Caccone, A. (2009). Characterization of a nonclassical class I MHC gene in a reptile, the Galapagos Marine Iguana (Amblyrhynchus cristatus). PLOS One, 3(8), e2859.
   Web of Science ®Google Scholar
• Grimholt, U., Tsukamoto, K., Azuma, T., Leong, J., Koop, B. F., & Dijkstra, J. M. (2015). A comprehensive analysis of teleost MHC class I sequences. BMC Evolutionary Biology, 15(32), 1–17.
   PubMedGoogle Scholar
• Grueber, C. E., Wallis, G. P., & Jamieson, I. G. (2014). Episodic positive selection in the evolution of Avian toll-like receptor innate immunity genes. PLOS One, 9(3), e89632.
   PubMed Web of Science ®Google Scholar
• Guindon, S., & Gascuel, O. (2003). A simple, fast, and accurate algorithm to estimate large phylogenies by maximum likelihood. Systematic Biology, 52(5), 696–704.
   PubMed Web of Science ®Google Scholar
• Hacking, J., Bertozzi, T., Moussalli, A., Bradford, T., & Gardner, M. (2018). Characterisation of major histocompatibility complex class I transcripts in an Australian dragon lizard. Developmental & Comparative Immunology, 84, 164–171.
   PubMed Web of Science ®Google Scholar
• Hacking, J., Stuart-Fox, D., & Gardner, M. (2018). Very low rate of multiple paternity detected in clutches of a wild agamid lizard. Australian Journal of Zoology, 65(5), 328–334.
   Web of Science ®Google Scholar
• Herdegen, M., Babik, W., & Radwan, J. (2014). Selective pressures on MHC class II genes in the guppy (Poecilia reticulata) as inferred by hierarchical analysis of population structure. Journal of Evolutionary Biology, 27(11), 2347–2359.
   PubMed Web of Science ®Google Scholar
• Janeway, C. J., Travers, P., & Walport, M. (2001). Immunobiology: The immune system in health and disease (5th ed.). New York: Garland Science.
   Google Scholar
• Kaufman, J. (2015). What chickens would tell you about the evolution of antigen processing and presentation. Current Opinion in Immunology, 34, 35–42.
   PubMed Web of Science ®Google Scholar
• Kaufman, J., Salomonsen, J., & Flajnik, M. (1994). Evolutionary conservation of MHC class I and class II molecules: Different yet the same. Seminars Immunology, 6, pp. 411–424.
   Google Scholar
• Kaufman, J., Volk, H., & Wallny, H. J. (1995). A “minimal essential MHC” and an “unrecognized MHC”: Two extremes in selection for polymorphism. Immunological Reviews, 143(1), 63–88.
   PubMedGoogle Scholar
• Kearse, M., Moir, R., Wilson, A., Stones-Havas, S., Cheung, M., Sturrock, S., … Drummond, A. (2010). Datamonkey 2010: A suite of phylogenetic analysis tools for evolutionary biology. Bioinformatics, 26(19), 2455–2457.
   Web of Science ®Google Scholar
• Kiemnec-Tyburczy, K., Richmond, J., Savage, A., Lips, K., & Zamudio, K. (2012). Genetic diversity of MHC class I loci in six non-model frogs is shaped by positive selection and gene duplication. Heredity, 109(3), 146–155.
   PubMed Web of Science ®Google Scholar
• Kosakovsky Pond, S. L., & Frost, S. D. (2005). Not so different after all: A comparison of methods for detecting amino acid sites under selection. Molecular Biology and Evolution, 22(5), 1208–1222.
   PubMed Web of Science ®Google Scholar
• Lanfear, R., Calcott, B., Ho, S. Y., & Guindon, S. (2012). Partitionfinder: Combined selection of partitioning schemes and substitution models for phylogenetic analyses. Molecular Biology and Evolution, 29(6), 1695–1701.
   PubMed Web of Science ®Google Scholar
• Lanfear, R., Frandsen, P. B., Wright, A. M., Senfeld, T., & Calcott, B. (2017). Partitionfinder 2: New methods for selecting partitioned models of evolution for molecular and morphological phylogenetic analyses. Molecular Biology and Evolution, 34(3), 772–773.
   PubMed Web of Science ®Google Scholar
• Lenz, T., & Becker, S. (2008). Simple approach to reduce PCR artefact formation leads to reliable genotyping of MHC and other highly polymorphic loci–Implications for evolutionary analysis. Gene, 427(1–2), 117–123.
   PubMed Web of Science ®Google Scholar
• Lighten, J., Oosterhout, C., & Bentzen, P. (2014). Critical review of NGS analyses for de novo genotyping multigene families. Molecular Ecology, 2014(23), 3957–3972.
   Google Scholar
• Liu, L., Li, Y., Li, S., Hu, N., He, Y., Pong, R., … Law, M. (2012). Comparison of next-generation sequencing systems. Journal of Biomedicine & Biotechnology, 2012, 251–364.
   Google Scholar
• Llaurens, V., McMullan, M., & van Oosterhout, C. (2012). Cryptic MHC polymorphism revealed but not explained by selection on the class iib peptide-binding region. Molecular Biology and Evolution, 29(6), 1631–1644.
   PubMed Web of Science ®Google Scholar
• Loman, N., Misra, R., Dallman, T., Constantinidou, C., Gharbia, S., Wain, J., & Pallen, M. (2012). Performance comparison of benchtop high-throughput sequencing platforms. Nature Biotechnology, 30(2012), 434–439.
   PubMedGoogle Scholar
• Marmesat, E., Soriano, L., Mazzoni, C. J., Sommer, S., & Godoy, J. A. (2016). PCR strategies for complete allele calling in multigene families using high-throughput sequencing approaches. PLOS One, 11(6), e0157402.
   PubMed Web of Science ®Google Scholar
• McLean, C. A., Moussalli, A., & Stuart-Fox, D. (2013). Taxonomic assessment of the Ctenophorus decresii complex (Reptilia: Agamidae) reveals a new species of dragon lizard from western New South Wales. Records of the Australian Museum, 65(3), 51–63.
   Web of Science ®Google Scholar
• McLean, C. A., Stuart-Fox, D., & Moussalli, A. (2014). Phylogeographic structure, demographic history and morph composition in a colour polymorphic lizard. Journal of Evolutionary Biology, 27(10), 2123–2137.
   PubMed Web of Science ®Google Scholar
• Miller, H. C., Andrews-Cookson, M., & Daugherty, C. H. (2007). Two patterns of variation among MHC class I loci in Tuatara (Sphenodon punctatus). Journal of Heredity, 98(7), 666–677.
   PubMed Web of Science ®Google Scholar
• Murrell, B., Wertheim, J. O., Moola, S., Weighill, T., Scheffler, K., & Pond, S. K. (2012). Detecting individual sites subject to episodic diversifying selection. PLOS Genetics, 8(7), e1002764.
   PubMed Web of Science ®Google Scholar
• Ohta, Y., Goetz, W., Hossain, M. Z., Nonaka, M., & Flajnik, M. F. (2006). Ancestral organization of the MHC revealed in the amphibian Xenopus. Journal of Immunology, 176(6), 3674–3685.
   PubMed Web of Science ®Google Scholar
• Pearson, S., Bradford, T., Ansari, T., Bull, M., & Gardner, M. (2016). MHC genotyping from next-generation sequencing: Detailed methodology for the gidgee skink, Egernia stokesii. Transactions of the Royal Society of South Australia, 140(2), 244–262.
   Web of Science ®Google Scholar
• Pearson, S. K., Bull, C., & Gardner, M. (2016). Egernia stokesii (gidgee skink) MHC I positively selected sites lack concordance with HLA peptide binding regions. Immunogenetics, 69(1), 49–61.
   PubMed Web of Science ®Google Scholar
• Piertney, S., & Oliver, M. (2006). The evolutionary ecology of the major histocompatibility complex. Heredity, 96(1), 7–21.
   PubMed Web of Science ®Google Scholar
• R Core Team. (2016). R: A language and environment for statistical computing. Vienna, Austria: R Foundation for Statistical Computing. Retrieved from https://www.R-project.org/
   Google Scholar
• Radwan, J., Kuduk, K., Levy, E., LeBas, N., & Babik, W. (2014). Parasite load and MHC diversity in undisturbed and agriculturally modified habitats of the ornate dragon lizard. Molecular Ecology, 23(24), 5966–5978.
   PubMed Web of Science ®Google Scholar
• Rambaut, A. (2012). FigTree (Version 1.4.2). Institute of Evolutionary Biology, University of Edinburgh. Retrieved from http://tree.bio.ed.ac.uk/
   Google Scholar
• Reche, P. A., & Reinherz, E. L. (2003). Sequence variability analysis of human class I and class II MHC molecules: Functional and structural correlates of amino acid polymorphisms. Journal of Molecular Biology, 331(3), 623–641.
   PubMed Web of Science ®Google Scholar
• Ronquist, F., Teslenko, P., Ayres, D., Darling, S., Hohna, S., Larget, B., … Huelsenbeck, J. P. (2011). MrBayes 3.2: Efficient Bayesian phylogenetic inference and model choice across a large model space. Systematic Biology, 6(3), 539–542.
   Google Scholar
• Ross, M. G., Russ, C., Costello, M., Hollinger, A., Lennon, N. J., Hegarty, R., … Jaffe, D. B. (2013). Characterizing and measuring bias in sequence data. Genome Biology, 14(5), 1–20.
   Web of Science ®Google Scholar
• Schnell, I., Bohmann, K., & Gilbert, M. (2015). Tag jumps illuminated – Reducing sequence-to-sample misidentifications in metabarcoding studies. Molecular Ecology Resources, 15(6), 1289–1303.
   PubMed Web of Science ®Google Scholar
• Schrider, D., & Hahn, M. (2010). Gene copy-number polymorphism in nature. Proceedings of the Royal Society B: Biological Sciences, 2010(277), 3213–3221.
   Google Scholar
• Sebastian, A., Herdegen, M., Migalska, M., & Radwan, J. (2016). AMPLISAS: A web server for multilocus genotyping using next-generation amplicon sequencing data. Molecular Ecology, 16(2), 498–510.
   Web of Science ®Google Scholar
• Smith, L., & Burgoyne, L. (2004). Collecting, archiving and processing DNA from wildlife samples using FTA® databasing paper. BMC Ecology, 4(1), 4.
   PubMedGoogle Scholar
• Sommer, S., Courtiol, A., & Mazzoni, C. (2013). MHC genotyping of non-model organisms using next-generation sequencing: A new methodology to deal with artefacts and allelic dropout. BMC Genomics, 14(1), 542.
   PubMedGoogle Scholar
• Strandh, M., Lannefors, M., Bonadonna, F., & Westerdahl, H. (2011). Characterization of MHC class I and II genes in a subantarctic seabird, the blue petrel, Halobaena caerulea (Procellariiformes). Immunogenetics, 63(10), 653–666.
   PubMed Web of Science ®Google Scholar
• Stutz, W., & Bolnick, D. (2014). Stepwise threshold clustering: A new method for genotyping MHC loci using next-generation sequencing technology. PLOS One, 9(7), e100587.
   PubMed Web of Science ®Google Scholar
• Wang, D., Zhong, L., Wei, Q., Gan, X., & He, S. (2010). Evolution of MHC class I genes in two ancient fish, paddlefish (Polyodon spathula) and Chinese sturgeon (Acipenser sinensis). FEBS letters, 584(15), 3331–3339.
   PubMed Web of Science ®Google Scholar
• Wang, X. X., & He, X. X. (2006). Summary of the evolution studies on primate major histocompatibility complex class I. Hereditas, 28(5), 611–616.
   PubMedGoogle Scholar
• Zagalska-Neubauer, M., Babik, W., Stuglik, M., Gustafsson, L., Cichon, M., & Radwan, J. (2010). 454 sequencing reveals extreme complexity of the class II major histocompatibility complex in the collared flycatcher. BMC Evolutionary Biology, 10(395), 1–15.
   PubMedGoogle Scholar