Akaike H (1973) Maximum likelihood identification of Gaussian autoregressive moving average models. Biometrika 60:255–265

Article  Google Scholar 

Alcaide M, Edwards SV (2011) Molecular evolution of the toll-like receptor multigene family in birds. Mol Biol Evol 28:1703–1715

Article  CAS  PubMed  Google Scholar 

Anderson TK, Macken CA, Lewis NS, et al (2016) A phylogeny-based global nomenclature system and automated annotation tool for H1 hemagglutinin genes from swine influenza A viruses. mSphere 1. https://doi.org/10.1128/mSphere.00275-16

Babik W, Dudek K, Fijarczyk A et al (2014) Constraint and adaptation in newt toll-like receptor genes. Genome Biol Evol 7:81–95

Article  PubMed  PubMed Central  Google Scholar 

Benton MJ, Wilf P, Sauquet H (2022) The Angiosperm Terrestrial Revolution and the origins of modern biodiversity. New Phytol 233:2017–2035

Article  PubMed  Google Scholar 

Beutler B, Rehli M (2002) Evolution of the TIR, tolls and TLRs: functional inferences from computational biology. Curr Top Microbiol Immunol 270:1–21

CAS  PubMed  Google Scholar 

Boehm T (2012) Evolution of vertebrate immunity. Curr Biol 22:R722–R732

Article  CAS  PubMed  Google Scholar 

Boehm T, Swann JB (2014) Origin and evolution of adaptive immunity. Annu Rev Anim Biosci 2:259–283

Article  CAS  PubMed  Google Scholar 

Bollback JP (2006) SIMMAP: stochastic character mapping of discrete traits on phylogenies. BMC Bioinformatics 7:88

Article  PubMed  PubMed Central  Google Scholar 

Boudinot P, Zou J, Ota T et al (2014) A tetrapod-like repertoire of innate immune receptors and effectors for coelacanths. J Exp Zool B Mol Dev Evol 322:415–437

Article  CAS  PubMed  Google Scholar 

Braasch I, Gehrke AR, Smith JJ et al (2016) The spotted gar genome illuminates vertebrate evolution and facilitates human-teleost comparisons. Nat Genet 48:427–437

Article  CAS  PubMed  PubMed Central  Google Scholar 

Bradford YM, Van Slyke CE, Ruzicka L, et al (2022) Zebrafish information network, the knowledgebase for Danio rerio research. Genetics 220. https://doi.org/10.1093/genetics/iyac016

Buchmann K (2014) Evolution of innate immunity: clues from invertebrates via fish to mammals. Front Immunol 5:459

Article  PubMed  PubMed Central  Google Scholar 

Buckley KM, Rast JP (2015) Diversity of animal immune receptors and the origins of recognition complexity in the deuterostomes. Dev Comp Immunol 49:179–189

Article  CAS  PubMed  Google Scholar 

Carlson KB, Wcisel DJ, Ackerman HD, et al (2022) Transcriptome annotation reveals minimal immunogenetic diversity among Wyoming toads, Anaxyrus Baxteri

Casadevall A, Damman C (2020) Updating the fungal infection-mammalian selection hypothesis at the end of the Cretaceous Period. PLoS Pathog 16:e1008451

Article  CAS  PubMed  PubMed Central  Google Scholar 

Clemente N, Raineri D, Cappellano G et al (2016) Osteopontin bridging innate and adaptive immunity in autoimmune diseases. J Immunol Res 2016:7675437

Article  PubMed  PubMed Central  Google Scholar 

Cooper MD, Alder MN (2006) The evolution of adaptive immune systems. Cell 124:815–822

Article  CAS  PubMed  Google Scholar 

Corrochano LM (2019) Light in the fungal world: from photoreception to gene transcription and beyond. Annu Rev Genet 53:149–170

Article  CAS  PubMed  Google Scholar 

Cunliffe J (2006) Tissue homeostasis and immunity – more on models. Scand J Immunol 64:172–176

Article  CAS  PubMed  Google Scholar 

Dornburg A, Mallik R, Wang Z et al (2022) Placing human gene families into their evolutionary context. Hum Genomics 16:56

Article  PubMed  PubMed Central  Google Scholar 

Dornburg A, Near TJ (2021) The emerging phylogenetic perspective on the evolution of actinopterygian fishes. Annu Rev Ecol Evol Syst 52:427–452

Article  Google Scholar 

Dornburg A, Townsend JP, Brooks W et al (2017) New insights on the sister lineage of percomorph fishes with an anchored hybrid enrichment dataset. Mol Phylogenet Evol 110:27–38

Article  PubMed  Google Scholar 

Dornburg A, Wang Z, Wang J, et al (2021a) Comparative genomics within and across bilaterians illuminates the evolutionary history of ALK and LTK proto-oncogene origination and diversification. Genome Biol Evol 13. https://doi.org/10.1093/gbe/evaa228

Dornburg A, Wcisel DJ, Zapfe K et al (2021b) Holosteans contextualize the role of the teleost genome duplication in promoting the rise of evolutionary novelties in the ray-finned fish innate immune system. Immunogenetics 73:479–497

Article  CAS  PubMed  PubMed Central  Google Scholar 

Dornburg A, Yoder JA (2022) On the relationship between extant innate immune receptors and the evolutionary origins of jawed vertebrate adaptive immunity. Immunogenetics 74:111–128

Article  CAS  PubMed  Google Scholar 

Dowse TJ, Soldati D (2005) Rhomboid-like proteins in Apicomplexa: phylogeny and nomenclature. Trends Parasitol 21:254–258

Article  CAS  PubMed  Google Scholar 

Du K, Stöck M, Kneitz S et al (2020) The sterlet sturgeon genome sequence and the mechanisms of segmental rediploidization. Nat Ecol Evol 4:841–852

Article  PubMed  PubMed Central  Google Scholar 

Eddy SR (2009) A new generation of homology search tools based on probabilistic inference. Genome Inform 23:205–211

PubMed  Google Scholar 

Edelman GM, Gall WE (1969) The antibody problem. Annu Rev Biochem 38:415–466

Article  CAS  PubMed  Google Scholar 

El-Zayat SR, Sibaii H, Mannaa FA (2019) Toll-like receptors activation, signaling, and targeting: an overview. Bull Natl Res Cent 43. https://doi.org/10.1186/s42269-019-0227-2

Fernández R, Gabaldón T (2020) Gene gain and loss across the metazoan tree of life. Nat Ecol Evol 4:524–533

Article  PubMed  PubMed Central  Google Scholar 

Flajnik MF (2018) A cold-blooded view of adaptive immunity. Nat Rev Immunol 18:438–453

Article  CAS  PubMed  PubMed Central  Google Scholar 

Gallucci S, Maffei ME (2017) DNA Sensing across the Tree of Life. Trends Immunol 38:719–732

Article  CAS  PubMed  Google Scholar 

Ghezelayagh A, Harrington RC, Burress ED et al (2022) Prolonged morphological expansion of spiny-rayed fishes following the end-Cretaceous. Nat Ecol Evol 6:1211–1220

Article  PubMed  Google Scholar 

Gianchecchi E, Delfino DV, Fierabracci A (2018) NK cells in autoimmune diseases: Linking innate and adaptive immune responses. Autoimmun Rev 17:142–154

Article  CAS  PubMed  Google Scholar 

Giles S, Xu G-H, Near TJ, Friedman M (2017) Early members of “living fossil” lineage imply later origin of modern ray-finned fishes. Nature 549:265–268

Article  CAS  PubMed  Google Scholar 

Gong J, Wei T, Zhang N et al (2010) TollML: a database of toll-like receptor structural motifs. J Mol Model 16:1283–1289

Article  CAS  PubMed  Google Scholar 

Hansson BS, Stensmyr MC (2011) Evolution of Insect Olfaction. Neuron 72:698–711

Article  CAS  PubMed  Google Scholar 

Höhne C, Prokopov D, Kuhl H et al (2021) The immune system of sturgeons and paddlefish (Acipenseriformes): a review with new data from a chromosome-scale sturgeon genome. Rev Aquac 13:1709–1729

Article  Google Scholar 

Huang S, Chen Z, Yan X et al (2014) Decelerated genome evolution in modern vertebrates revealed by analysis of multiple lancelet genomes. Nat Commun 5:5896

Article  CAS  PubMed  Google Scholar 

Huang Y, Temperley ND, Ren L et al (2011) Molecular evolution of the vertebrate TLR1 gene family - a complex history of gene duplication, gene conversion, positive selection and co-evolution. BMC Evol Biol 11:1–17

Article  CAS  Google Scholar 

Hughes AL (2010) Origin and diversification of the L-amino oxidase family in innate immune defenses of animals. Immunogenetics 62:753–759

Article  CAS  PubMed  PubMed Central  Google Scholar 

Hughes GM, Boston ESM, Finarelli JA et al (2018a) The birth and death of olfactory receptor gene families in mammalian niche adaptation. Mol Biol Evol 35:1390–1406

Article  CAS  PubMed