References

Ahn, M., Anderson, D. E., Zhang, Q., Tan, C. W., Lim, B. L., Luko, K., … Wang, L. F. (2019). Dampened NLRP3-mediated inflammation in bats and implications for a special viral reservoir host. Nature Microbiology, 4, 789-799. doi: 10.1038/s41564-019-0371-3
Ahn, M., Cui, J., Irving, A. T., & Wang, L. F. (2016). Unique loss of the PYHIN gene family in bats amongst mammals: Implications for inflammasome sensing. Scientific Reports, 6 . doi: 10.1038/srep21722
Amitai, O., Holtze, S., Barkan, S., Amichai, E., Korine, C., Pinshow, B., & Voigt, C. C. (2010). Fruit bats (Pteropodidae) fuel their metabolism rapidly and directly with exogenous sugars. The Journal of Experimental Biology, 213 (215), 2693-2699. doi: 10.1242/jeb.043505
Arapović, J., Lenac, T., Antulov, R., Polić, B., Ruzsics, Z., Carayannopoulos, L. N., … Jonjić, S. (2009). Differential Susceptibility of RAE-1 Isoforms to Mouse Cytomegalovirus. Journal of Virology, 83 (16), 8198-8207. doi: 10.1128/jvi.02549-08
Akbar, A . N., & Gilroy, D. W. (2020). Aging immunity may exacerbate COVID-19. Science, 369 (6501), 256-257. doi.org/10.1126/science.abb0762
Ashburner, M., Ball, C. A., Blake, J. A., Botstein, D., Butler, H., Cherry, J. M., … Sherlock, G. (2000). Gene ontology: Tool for the unification of biology. Nature Genetics, 25, 25-29. doi: 10.1038/75556
Austad, S. N., & Fischer, K. E. (1991). Mammalian aging, metabolism, and ecology: Evidence from the bats and marsupials. Journals of Gerontology, 46 (2),47-53. doi: 10.1093/geronj/46.2.B47
Ayala-Berdon, J., & Schondube, J. E. (2011). A physiological perspective on nectar-feeding adaptation in phyllostomid bats.Physiological and Biochemical Zoology . 84, 458-466. doi: 10.1086/661541
Babic, A. M., Wang, H. W., Lai, M. J., Daniels, T. G., Felbinger, T. W., Burger, P. C., … Wagner, D. D. (2004). ICAM-1 and β2 integrin deficiency impairs fat oxidation and insulin metabolism during fasting.Molecular Medicine, 10 (7-12), 72-79. doi: 10.2119/2004-00038.Wagner
Baker, M. L., & Schountz, T. (2018). Mammalia: Chiroptera: Immunology of Bats. In E. Cooper (Eds.),. Springer International Publishing(pp. 869-832). doi.org/10.1007/978-3-319-76768-0_23
Banerjee, A., Baker, M. L., Kulcsar, K., Misra, V., Plowright, R., & Mossman, K. (2020). Novel Insights Into Immune Systems of Bats.Frontiers in Immunology, 11, 1-26. doi: 10.3389/fimmu.2020.00026
Banerjee, A., Rapin, N., Bollinger, T., & Misra, V. (2017). Lack of inflammatory gene expression in bats: A unique role for a transcription repressor. Scientific Reports 7, 1-15. doi: 10.1038/s41598-017-01513-w
Banerjee, M., Mehr, R., Belelovsky, A., Spencer, J., & Dunn-Walters, D. K. (2002). Age- and tissue-specific differences in human germinal center B cell selection revealed by analysis of IgVH gene hypermutation and lineage trees. European Journal of Immunology , 32 (7), 1947–1957. doi: 10.1002/1521-4141(200207)32:7<1947::AID-IMMU1947>3.0.CO;2-1
Basler, C. (2020). Innate Immunity in Bats. In Eugenia Corrales-Aguilar & M. Schwemmle (Eds.), Bats and Viruses: Current Research and Future Trends (pp. 119–134). Caister Academic Press. doi:10.21775/9781912530144.08
Bateman, A. (2019). UniProt: A worldwide hub of protein knowledge.Nucleic Acids Research, 47 (D1), D506-D515. doi: 10.1093/nar/gky1049
Bay, R. A., Rose, N. H., Logan, C. A., & Palumbi, S. R. (2017). Genomic models predict successful coral adaptation if future ocean warming rates are reduced. Science Advances, 3 (11). doi: 10.1126/sciadv.1701413
Berg, J., Tymoczko, J., & Stryer, L. (2002). Biochemistry (5th ed.). New York: WH Freeman.
Bernatchez, L., & Landry, C. (2003). MHC studies in nonmodel vertebrates: What have we learned about natural selection in 15 years?Journal of Evolutionary Biology, 16 (3), 363-377. doi: 10.1046/j.1420-9101.2003.00531.x
Bhattacharya, S., Andorf, S., Gomes, L., Dunn, P., Schaefer, H., Pontius, J., … Butte, A. J. (2014). ImmPort: Disseminating data to the public for the future of immunology. Immunologic Research, 58, 234-239. doi: 10.1007/s12026-014-8516-1
Boni, M. F., Lemey, P., Jiang, X., Lam, T. T. Y., Perry, B. W., Castoe, T. A., … Robertson, D. L. (2020). Evolutionary origins of the SARS-CoV-2 sarbecovirus lineage responsible for the COVID-19 pandemic.Nature Microbiology, 5, 1408-1417. doi: 10.1038/s41564-020-0771-4
Brook, C. E., & Dobson, A. P. (2015). Bats as “special” reservoirs for emerging zoonotic pathogens. Trends in Microbiology, 23 (3), 172-180. doi: 10.1016/j.tim.2014.12.004
Camacho, C., Coulouris, G., Avagyan, V., Ma, N., Papadopoulos, J., Bealer, K., & Madden, T. L. (2009). BLAST+: Architecture and applications. BMC Bioinformatics, 10 (421). doi: 10.1186/1471-2105-10-421
Carbon, S., Douglass, E., Dunn, N., Good, B., Harris, N. L., Lewis, S. E., … Westerfield, M. (2019). The Gene Ontology Resource: 20 years and still GOing strong. Nucleic Acids Research, 47 (D1), D330-D338. doi: 10.1093/nar/gky1055
Costantini, D., Lindecke, O., Petersons, G., & Voigt, C. C. (2019). Migratory flight imposes oxidative stress in bats. Current Zoology, 65 (2), 147-153. doi: 10.1093/cz/zoy039
Czaplewski, N. J. (2010). Bats ( Mammalia : Chiroptera ) from Gran Barranca ( early Miocene , Colhuehuapian ), Chubut Province , Argentina. In Madden, R., Carlini, A. A., Guiomar, V. M., & Kay, R. F.(Eds.),The Paleontology of Gran Barranca. Evolution and environmental change through the middle Cenozoic of Patagonia. (pp. 240–252). Cambridge University Press.
Czaplewski, Nicolas J, Takai, M., Naeher, T. M., & Setoguchi, T. (2003). Additional bats from the middle miocene la venta fauna of Colombia. Revista de la academia colombiana de ciencias, 27 (103), 263-282.
Darriba, D., Taboada, G. L., Doallo, R., & Posada, D. (2011). ProtTest 3: Fast selection of best-fit models of protein evolution.Bioinformatics (Oxford, England). 27 (8), 1164-1165. doi: 10.1093/bioinformatics/btr088
Davalos, L. M., Velazco, P. M., & Rojas, D. (2020). Phylogenetics and Historical Biogeography. In Phyllostomid bats: A Unique Mammalian Radiation (pp. 87–103). Chicago, University of Chicago Press.
Dávalos, L. M., Velazco, P. M., Warsi, O. M., Smits, P. D., & Simmons, N. B. (2014). Integrating incomplete fossils by isolating conflicting signal in saturated and non-independent morphological characters.Systematic Biology, 63 (4), 582-600. doi: 10.1093/sysbio/syu022
Davies, K. T. J., Yohe, L. R., Almonte, T., Sanchez, M. K. R., Rengifo, E. M., Dumont E. R., … Rossiter, S. J. (2020). Foraging shifts and visual preadaptation in ecologically diverse bats. Molecular Ecology , 28 (10), 1839-1859. https://doi.org/10.1111/mec.15445
Delves, P. J., Martin, S. J., Burton, D. R., & Roitt, I. M. (2017).Roitt’s Essential Immunology (13th edition). London, UK: Wiley Blackwell.
Denton, J. F., Lugo-Martinez, J., Tucker, A. E., Schrider, D. R., Warren, W. C., & Hahn, M. W. (2014). Extensive Error in the Number of Genes Inferred from Draft Genome Assemblies. PLoS Computational Biology, 10 (12). doi: 10.1371/journal.pcbi.1003998
Djelloul, M., Popa, N., Pelletier, F., Raguénez, G., & Boucraut, J. (2016). RAE-1 expression is induced during experimental autoimmune encephalomyelitis and is correlated with microglia cell proliferation.Brain, Behavior, and Immunity, 58, 209-217. doi: 10.1016/j.bbi.2016.07.147
Dong, D., Lei, M., Hua, P., Pan, Y. H., Mu, S., Zheng, G., … Zhang, S. (2017). The genomes of two bat species with long constant frequency echolocation calls. Molecular Biology and Evolution, 34 (1), 20-34. doi: 10.1093/molbev/msw231
Dong, Z. M., Gutierrez-Ramos, J. C., Coxon, A., Mayadas, T. N., & Wagner, D. D. (1997). A new class of obesity genes encodes leukocyte adhesion receptors. Proceedings of the National Academy of Sciences of the United States of America, 94 (14), 7526-7530. doi: 10.1073/pnas.94.14.7526
Drexler, J. F., Corman, V. M., Müller, M. A., Maganga, G. D., Vallo, P., Binger, T., … Drosten, C. (2012). Bats host major mammalian paramyxoviruses. Nature Communications, 3 (796). doi: 10.1038/ncomms1796
Dumont, E. R., Dávalos, L. M., Goldberg, A., Santana, S. E., Rex, K., & Voigt, C. C. (2012). Morphological innovation, diversification and invasion of a new adaptive zone. Proceedings of the Royal Society B: Biological Sciences, 279 (1734). doi: 10.1098/rspb.2011.2005
Eckalbar, W. L., Schlebusch, S. A., Mason, M. K., Gill, Z., Parker, A. V., Booker, B. M., … Ahituv, N. (2016). Transcriptomic and epigenomic characterization of the developing bat wing. Nature Genetics, 48, 528-536. doi: 10.1038/ng.3537
Eiting, T. P., & Gunnell, G. F. (2009). Global completeness of the bat fossil record. Journal of Mammalian Evolution, 16, 151-173. doi: 10.1007/s10914-009-9118-x
Emms, D. M., & Kelly, S. (2019). OrthoFinder: Phylogenetic orthology inference for comparative genomics. Genome Biology, 20, 238. doi: 10.1186/s13059-019-1832-y
Feng, C. G., Zheng, L., Jankovic, D., Báfica, A., Cannons, J. L., Watford, W. T., … Sher, A. (2008). The immunity-related GTPase Irgm1 promotes the expansion of activated CD4+ T cell populations by preventing interferon-γ-induced cell death. Nature Immunology, 9,1279-1287. doi: 10.1038/ni.1653
Fenton, M. B., & Simmons, N. B. (2015). Bats: a world of science and mystery . Chicago, IL: The University of Chicago Press.
Ferber, I. A., Brocke, S., Taylor-Edwards, C., Ridgway, W., Dinisco, C., Steinman, L., … Fathman, C. G. (1996). Mice with a disrupted IFN-gamma gene are susceptible to the induction of experimental autoimmune encephalomyelitis (EAE). Journal of Immunology (Baltimore, Md. : 1950), 156 (1), 5-7.
Fleischer, T., Gampe, J. Scheuerlein, A., & Kerth, G. (2017). Rare catastrophic events drive population dynamics in a bat species with negligible senescence. Scientific reports, 7, 7370. doi.org/10.1038/s41598-017-06392-9
Foley, N. M., Hughes, G. M., Huang, Z., Clarke, M., Jebb, D., Whelan, C. V., … Teeling, E. C. (2018). Growing old, yet staying young: The role of telomeres in bat’s exceptional longevity. Genetics, 4.doi: 10.1126/sciadv.aao0926
Genereux, D. P., Serres, A., Armstrong, J., Johnson, J., Marinescu, V. D., Murén, E., … Karlsson, E. K. (2020). A comparative genomics multitool for scientific discovery and conservation. Nature, 587 , 240-245. doi: 10.1038/s41586-020-2876-6
Goebel, J., Promerová, M., Bonadonna, F., McCoy, K. D., Serbielle, C., Strandh, M., … Fumagalli, L. (2017). 100 million years of multigene family evolution: Origin and evolution of the avian MHC class IIB. BMC Genomics, 18, 460. doi: 10.1186/s12864-017-3839-7
Goldstein, T., Anthony, S. J., Gbakima, A., Bird, B. H., Bangura, J., Tremeau-Bravard, A., … Mazet, J. A. K. (2018). The discovery of Bombali virus adds further support for bats as hosts of ebolaviruses.Nature Microbiology, 3 , 1084-1089. doi: 10.1038/s41564-018-0227-2
Gorbunova, V., Seluanov, A., & Kennedy, B. K. (2020). The World Goes Bats: Living Longer and Tolerating Viruses. Cell Metabolism, 32 (1), 31-43. doi: 10.1016/j.cmet.2020.06.013
Grigat, J., Soruri, A., Forssmann, U., Riggert, J., & Zwirner, J. (2007). Chemoattraction of Macrophages, T Lymphocytes, and Mast Cells Is Evolutionarily Conserved within the Human α-Defensin Family. The Journal of Immunology, 179 (6), 3958-3965. doi: 10.4049/jimmunol.179.6.3958
Gunnell, G. F., & Simmons, N. B. (2005). Fossil evidence and the origin of bats. Journal of Mammalian Evolution, 12, 209-246. doi: 10.1007/s10914-005-6945-2
Gutiérrez-Guerrero, Y. T., Ibarra-Laclette, E., Martínez Del Río, C., Barrera-Redondo, J., Rebollar, E. A., Ortega, J., … Eguiarte, L. E. (2020). Genomic consequences of dietary diversification and parallel evolution due to nectarivory in leaf-nosed bats. GigaScience, 9 (6). doi:10.1093/gigascience/giaa059
Hahn, M. W., De Bie, T., Stajich, J. E., Nguyen, C., & Cristianini, N. (2005). Estimating the tempo and mode of gene family evolution from comparative genomic data. Genome Research, 15 (8), 1153-1160. doi: 10.1101/gr.3567505
Han, H. J., Wen, H. ling, Zhou, C. M., Chen, F. F., Luo, L. M., Liu, J. wei, & Yu, X. J. (2015). Bats as reservoirs of severe emerging infectious diseases. Virus Research, 505, 1-6. doi: 10.1016/j.virusres.2015.05.006
Han, M. V., Thomas, G. W. C., Lugo-Martinez, J., & Hahn, M. W. (2013). Estimating gene gain and loss rates in the presence of error in genome assembly and annotation using CAFE 3. Molecular Biology and Evolution, 30 (8), 1987-1997. doi: 10.1093/molbev/mst100
Harper, J. M., Salmon, A. B., Leiser, S. F., Galecki, A. T., & Miller, R. A. (2007). Skin-derived fibroblasts from long-lived species are resistant to some, but not all, lethal stresses and to the mitochondrial inhibitor rotenone. Aging Cell, 6 (1), 1-13. doi: 10.1111/j.1474-9726.2006.00255.x
Hayden, S., Bekaert, M., Goodbla, A., Murphy, W. J., Dávalos, L. M., & Teeling, E. C. (2014). A cluster of olfactory receptor genes linked to frugivory in bats. Molecular Biology and Evolution. 31 (4), 917-927. doi: 10.1093/molbev/msu043
Hayman, D. T. S. (2019). Bat tolerance to viral infections. Nature Microbiology, 4, 728-729. doi: 10.1038/s41564-019-0430-9
Hayward, J. A., Tachedjian, M., Cui, J., Cheng, A. Z., Johnson, A., Baker, M. L., … Tachedjian, G. (2018). Differential evolution of antiretroviral restriction factors in pteropid bats as revealed by APOBEC3 gene complexity. Molecular Biology and Evolution, 35 (7), 1626-1637. doi: 10.1093/molbev/msy048
Healy, K., Guillerme, T., Finlay, S., Kane, A., Kelly, S. B. A., McClean, D., … Cooper, N. (2014). Ecology and mode-of-life explain lifespan variation in birds and mammals. Proceedings of the Royal Society B: Biological Sciences, 281 (1784). doi: 10.1098/rspb.2014.0298
Holt, C., & Yandell, M. (2011). MAKER2: An annotation pipeline and genome-database management tool for second-generation genome projects.BMC Bioinformatics, 12, 491 . doi: 10.1186/1471-2105-12-491
Hu, B., Zeng, L. P., Yang, X. Lou, Ge, X. Y., Zhang, W., Li, B., … Shi, Z. L. (2017). Discovery of a rich gene pool of bat SARS-related coronaviruses provides new insights into the origin of SARS coronavirus. PLoS Pathogens . doi: 10.1371/journal.ppat.1006698
Huang, R., Grishagin, I., Wang, Y., Zhao, T., Greene, J., Obenauer, J. C., … Austin, C. P. (2019). The NCATS BioPlanet – An integrated platform for exploring the universe of cellular signaling pathways for toxicology, systems biology, and chemical genomics. Frontiers in Pharmacology, 10, 445. doi: 10.3389/fphar.2019.00445
Huang, Z., Whelan, C. V., Dechmann, D., & Teeling, E. C. (2020). Genetic variation between long-lived versus short-lived bats illuminates the molecular signatures of longevity. Aging, 12 (16), 15962-15977. doi: 10.18632/aging.103725
Huang, Z., Whelan, C. V., Foley, N. M., Jebb, D., Touzalin, F., Petit, E. J., … Teeling, E. C. (2019). Longitudinal comparative transcriptomics reveals unique mechanisms underlying extended healthspan in bats. Nature Ecology and Evolution, 3 (7), 1110-1120. doi: 10.1038/s41559-019-0913-3
Huelsmann, M., Hecker, N., Springer, M. S., Gatesy, J., Sharma, V., & Hiller, M. (2019). Genes lost during the transition from land to water in cetaceans highlight genomic changes associated with aquatic adaptations. Science Advances, 5 (9), eaaw6671. doi: 10.1126/sciadv.aaw6671
Hughes, G. M., Boston, E. S. M., Finarelli, J. A., Murphy, W. J., Higgins, D. G., & Teeling, E. C. (2018). The birth and death of olfactory receptor gene families in Mammalian niche adaptation.Molecular Biology and Evolution, 35 (6), 1390-1406. doi: 10.1093/molbev/msy028
Janeway, C. A., & Travers, M, W. (2001). The major histocompatibility complex and its functions. Immunobiology: The Immune System in Health and Disease . Retrieved from https://www.ncbi.nlm.nih.gov/books/NBK10757/
Jebb, D., Huang, Z., Pippel, M., Hughes, G. M., Lavrichenko, K., Devanna, P., … Teeling, E. C. (2020). Six reference-quality genomes reveal evolution of bat adaptations. Nature, 538 (7817), 578-584. doi: 10.1038/s41586-020-2486-3
Jones, K. E., Bininda-Emonds, O. R. P., & Gittleman, J. L. (2005). Bats, clocks, and rocks: diversification patterns in chiroptera.Evolution; international journal of organic evolution, 59 (10), 2243-2255. doi: 10.1554/04-635.1
Kacprzyk, J., Hughes, G. M., Palsson-McDermott, E., Quinn, S. R., Puechmaille, S. J., O’Neill, L. A. J. & Teeling, E. C. (2017). A potent anti-inflammatory response in bat macrophages may be linked to extended longevity and viral tolerance. Acta Chiropterologica. 19 (2), 219-228. doi: 10.3161/15081109ACC2017.19.2.001
Katoh, K., & Standley, D. M. (2013). MAFFT multiple sequence alignment software version 7: Improvements in performance and usability.Molecular Biology and Evolution, 30 (4), 772-780. doi: 10.1093/molbev/mst010
Kearse, M., Moir, R., Wilson, A., Stones-Havas, S., Cheung, M., Sturrock, S., … Drummond, A. (2012). Geneious Basic: An integrated and extendable desktop software platform for the organization and analysis of sequence data. Bioinformatics (Oxford, England), 28 (12), 1647-1649. doi:10.1093/bioinformatics/bts199
Kelm, D.H., Simon, R., Kuhlow, D., Voigt, C. C., Ristow M. (2011). High activity enables life on a high-sugar diet: blood glucose regulation in nectar-feeding bats. Proceedings of the Royal Society B: Biological Sciences, 278 (1724),3490-3496.doi.org/10.1098/rspb.2011.0465
Kolmogorov, M., Yuan, J., Lin, Y., & Pevzner, P. A. (2019). Assembly of long, error-prone reads using repeat graphs. Nature Biotechnology, 37 (5), 540-546. doi: 10.1038/s41587-019-0072-8
Korf, I. (2004). Gene finding in novel genomes. BMC Bioinformatics, 5, 59. doi: 10.1186/1471-2105-5-59
Kosakovsky Pond, S. L., Frost, S. D. W., & Muse, S. V. (2005). HyPhy: Hypothesis testing using phylogenies. Bioinformatics (Oxford, England), 21 (5), 676-679. doi: 10.1093/bioinformatics/bti079
Lau, S. K. P., Luk, H. K. H., Wong, A. C. P., Li, K. S. M., Zhu, L., Zirong, H., … Woo, P. C. Y. (2020). Possible Bat Origin of Severe Acute Respiratory Syndrome Coronavirus 2.Emerging infectious diseases, 26 (7), 1542-1547. doi: https://dx.doi.org/10.3201/eid2607.200092.
Lenartić, M., Jelenčić, V., Zafirova, B., Ožanič, M., Marečić, V., Jurković, S., … Polić, B. (2017). NKG2D Promotes B1a Cell Development and Protection against Bacterial Infection. The Journal of Immunology (Baltimore, Md. : 1950), 198 (4), 1531-1542. doi: 10.4049/jimmunol.1600461
Lewin, H. A., Robinson, G. E., Kress, W. J., Baker, W. J., Coddington, J., Crandall, K. A., … Zhang, G. (2018). Earth BioGenome Project: Sequencing life for the future of life. Proceedings of the National Academy of Sciences of the United States of America, 115 (17), 4325-4333. doi: 10.1073/pnas.1720115115
Liberles, S. D., & Buck, L. B. (2006). A second class of chemosensory receptors in the olfactory epithelium. Nature, 442 (7103), 645-650. doi: 10.1038/nature05066
McHeyzer-Williams, M., Okitsu, S., Wang, N., & McHeyzer-Williams, L. (2012). Molecular programming of B cell memory. Nature Reviews Immunology , 12 (1), 24–34. doi: 10.1038/nri3128
Meakin, P. J., Morrison, V. L., Sneddon, C. C., Savinko, T., Uotila, L., Jalicy, S. M., … Fagerholm, S. C. (2015). Mice lacking beta2-integrin function remain glucose tolerant in spite of insulin resistance, neutrophil infiltration and inflammation. PLoS ONE, 10 (9), e0138872. doi: 10.1371/journal.pone.0138872
Memish, Z. A., Perlman, S., Van Kerkhove, M. D., & Zumla, A. (2020). Middle East respiratory syndrome. Lancet (London, England), 395 (10229), 1063-1077. doi: 10.1016/S0140-6736(19)33221-0
Meng, F., Zhu, L., Huang, W., Irwin, D. M., & Zhang, S. (2016). Bats: Body mass index, forearm mass index, blood glucose levels and SLC2A2 genes for diabetes. Scientific Reports, 6, 29960. doi: 10.1038/srep29960
Merad, M., & Martin, J. C. (2020). Pathological inflammation in patients with COVID-19: a key role for monocytes and macrophages.Nature Reviews Immunology, 20 (6), 355-362. doi: 10.1038/s41577-020-0331-4
Mi, H., Muruganujan, A., Ebert, D., Huang, X., & Thomas, P. D. (2019). PANTHER version 14: More genomes, a new PANTHER GO-slim and improvements in enrichment analysis tools. Nucleic Acids Research, 47 (D1), D419-D426. doi: 10.1093/nar/gky1038
Miller, M. R., McMinn, R. J., Misra, V., Schountz, T., Müller, M. A., Kurth, A., & Munster, V. J. (2016). Broad and Temperature Independent Replication Potential of Filoviruses on Cells Derived from Old and New World Bat Species. Journal of Infectious Diseases, 214 (suppl 3), S297-S302. doi: 10.1093/infdis/jiw199
Minias, P., Pikus, E., Whittingham, L. A., & Dunn, P. O. (2019). Evolution of copy number at the MHC varies across the avian tree of life. Genome Biology and Evolution, 11 (1), 17-28. doi: 10.1093/gbe/evy253
Moratelli, R., & Calisher, C. H. (2015). Bats and zoonotic viruses: Can we confidently link bats with emerging deadly viruses? Memorias Do Instituto Oswaldo Cruz, 110 (1), 1-22. doi: 10.1590/0074-02760150048
Nagaoka, I., Niyonsaba, F., Tsutsumi-Ishii, Y., Tamura, H., & Hirata, M. (2008). Evaluation of the effect of human β-defensins on neutrophil apoptosis. International Immunology 20(4), 543–553. doi: 10.1093/intimm/dxn012
Ng, J. H. J., Tachedjian, M., Deakin, J., Wynne, J. W., Cui, J., Haring, V., … Baker, M. L. (2016). Evolution and comparative analysis of the bat MHC-I region. Scientific reports, 6, 21256. doi: 10.1038/srep21256
Niyonsaba, F., Ushio, H., Hara, M., Yokoi, H., Tominaga, M., Takamori, K., … Okumura, K. (2010). Antimicrobial Peptides Human β-Defensins and Cathelicidin LL-37 Induce the Secretion of a Pruritogenic Cytokine IL-31 by Human Mast Cells. The Journal of Immunology (Baltimore, Md. : 1950), 184 (7), 3526–3534. doi: 10.4049/jimmunol.0900712
Nogueira, R. M. R., Lima, I. P., Garbino, G. S. T., Moratelli, R., Tavares, V. C., Gregorin, R., & Peracchi, A. L. (2018). No Updated checklist of Brazilian bats: version 2018. Comitê da Lista de Morcegos do Brasil-CLMB. Retrieved from Sociedade Brasileira para o Estudo de Quiropteros Retrieved from https://www.sbeq.net/lista-de-especies
Nowak, M. D., Birkeland, S., Mandáková, T., Roy Choudhury, R., Guo, X., Gustafsson, A. L. S., … Brochmann, C. (2020). The genome of Draba nivalis shows signatures of adaptation to the extreme environmental stresses of the Arctic. Molecular Ecology Resources . doi: 10.1111/1755-0998.13280
Olival, K. J., Hosseini, P. R., Zambrana-Torrelio, C., Ross, N., Bogich, T. L., & Daszak, P. (2017). Host and viral traits predict zoonotic spillover from mammals. Nature, 546(7660), 646–650 . doi: 10.1038/nature22975
Papenfuss, A. T., Baker, M. L., Feng, Z. P., Tachedjian, M., Crameri, G., Cowled, C., … Wang, L. F. (2012). The immune gene repertoire of an important viral reservoir, the Australian black flying fox.BMC Genomics , 13 (1). doi: 10.1186/1471-2164-13-261
Papkou, A., Guzella, T., Yang, W., Koepper, S., Pees, B., Schalkowski, R., … Schulenburg, H. (2019). The genomic basis of red queen dynamics during rapid reciprocal host–pathogen coevolution.Proceedings of the National Academy of Sciences of the United States of America, 116 (3), 923–928.. doi: 10.1073/pnas.1810402116
Parker, J., Tsagkogeorga, G., Cotton, J. A., Liu, Y., Provero, P., Stupka, E., & Rossiter, S. J. (2013). Genome-wide signatures of convergent evolution in echolocating mammals. Nature, 502 (7470), 228–231. doi: 10.1038/nature12511
Parthasarathy, R., Parthasarathy, L., & Vadnal, R. (1997). Brain inositol monophosphatase identified as a galactose 1-phosphatase.Brain Research, 778 (1), 99–106. doi: 10.1016/S0006-8993(97)01042-1
Pavlovich, S. S., Lovett, S. P., Koroleva, G., Guito, J. C., Arnold, C. E., Nagle, E. R., … Palacios, G. (2018). The Egyptian Rousette Genome Reveals Unexpected Features of Bat Antiviral Immunity.Cell, 173 (5), 1098–1110.e18. doi: 10.1016/j.cell.2018.03.070
Pickering, A. M., Lehr, M., Kohler, W. J., Han, M. L., & Miller, R. A. (2014). Fibroblasts from longer-lived species of primates, rodents, bats, carnivores, and birds resist protein damage. Journals of Gerontology - Series A Biological Sciences and Medical Sciences, 70 (7), 791–799. doi: 10.1093/gerona/glu115
Pierce, C. A., Preston-Hurlburt, P., Dai, Y., Aschner, C. B., Cheshenko, N., Galen, B., … Herold, B. C. (2020). Immune responses to SARS-CoV-2 infection in hospitalized pediatric and adult patients.Science Translational Medicine , 12 (564), eabd5487. doi: 10.1126/scitranslmed.abe8120
Podlutsky, A. J., Khritankov, A. M., Ovodov, N. D., & Austad, S. N. (2005). A new field record for bat longevity. The journals of gerontology, 60 (11), 1366-1368. doi.org/10.1093/gerona/60.11.1366
Pomaznoy, M., Ha, B., & Peters, B. (2018). GOnet: A tool for interactive Gene Ontology analysis. BMC Bioinformatics, 19 (1), 470. doi: 10.1186/s12859-018-2533-3
Potter, J., Davies, K., Yohe, L. R., Struebig, M., Warren, K., Tsagkogeorga, G., … Rossiter, S. J. (in press). Dietary diversification and specialisation in New World bats facilitated by early molecular evolution. Molecular Biology and Evolution .
Rafikov, R., McBride, M. L., Zemskova, M., Kurdyukov, S., McClain, N., Niihori, M., … Rafikova, O. (2019). Inositol monophosphatase 1 as a novel interacting partner of RAGE in pulmonary hypertension.American Journal of Physiology - Lung Cellular and Molecular Physiology, 316 (3), L428–L444. doi: 10.1152/ajplung.00393.2018
Rapista, A., Ding, J., Benito, B., Lo, Y. T., Neiditch, M. B., Lu, W., & Chang, T. L. (2011). Human defensins 5 and 6 enhance HIV-1 infectivity through promoting HIV attachment. Retrovirology, 8,45. doi: 10.1186/1742-4690-8-45
Ravel, A., Adaci, M., Bensalah, M., Charruault, A.-L., Essid, E. M., AMmar, H. K., … Marivaux, L. (2016). Origine et radiation initiale des chauves-souris modernes : nouvelles découvertes dans l’Éocène d’Afrique du Nord. Geodiversitas, 38 (3), 355-434. doi: 10.5252/g2016n3a3
Reddy, S. T., Ge, X., Miklos, A. E., Hughes, R. A., Kang, S. H., Hoi, K. H., … Georgiou, G. (2010). Monoclonal antibodies isolated without screening by analyzing the variable-gene repertoire of plasma cells.Nature Biotechnology , 28 (9), 965–969. doi: 10.1038/nbt.1673
Rhie, A., Mccarthy, S. A., Fedrigo, O., Damas, J., Formenti, G., London, S. E., … Friedrich, S. R. (2020). Towards complete and error-free genome assemblies of all vertebrate species. BioRxiv, 1–56. doi:10.1101/2020.05.22.110833
Rojas, D., Ramos Pereira, M. J., Fonseca, C., & Dávalos, L. M. (2018). Eating down the food chain: generalism is not an evolutionary dead end for herbivores. Ecology Letters, 21 (3), 402–410.. doi: 10.1111/ele.12911
Salmon, A. B., Leonard, S., Masamsetti, V., Pierce, A., Podlutsky, A. J., Podlutskaya, N., … Chaudhuri, A. R. (2009). The long lifespan of two bat species is correlated with resistance to protein oxidation and enhanced protein homeostasis. FASEB journal : official publication of the Federation of American Societies for Experimental Biology, 23 (7), 2317–2326. doi: 10.1096/fj.08-122523
Santos, P. S. C., Courtiol, A., Heidel, A. J., Höner, O. P., Heckmann, I. Nagy, … Sommer S. (2016). MHC-dependent mate choice is linked to a trace-amine-associated receptor gene in a mammal. Scientific Reports, 6, 38490. doi.org/10.1038/srep38490
Scheben, A., Ramos, O. M., Kramer, M., Goodwin, S., Oppenheim, S., Becker, D. J., … Mccombie, R. (2020). Unraveling molecular mechanisms of immunity and cancer-resistance using the genomes of the Neotropical bats Artibeus jamaicensis and Pteronotus mesoamericanus.BioRxiv . doi.org/10.1101/2020.09.09.290502
Schountz, T., Baker, M. L., Butler, J., & Munster, V. (2017). Immunological control of viral infections in bats and the emergence of viruses highly pathogenic to humans. Frontiers in Immunology, 8 , 1098. doi: 10.3389/fimmu.2017.01098
Schroder, K., Hertzog, P. J., Ravasi, T., & Hume, D. A. (2004). Interferon-γ: an overview of signals, mechanisms and functions.Journal of Leukocyte Biology, 75 (2), 163–189. doi: 10.1189/jlb.0603252
Seim, I., Fang, X., Xiong, Z., Lobanov, A. V., Huang, Z., Ma, S., … Gladyshev, V. N. (2013). Genome analysis reveals insights into physiology and longevity of the Brandt’s bat Myotis brandtii.Nature Communications, 4 ,2212. doi: 10.1038/ncomms3212
Semple, F., & Dorin, J. R. (2012). β-Defensins: Multifunctional modulators of infection, inflammation and more? Journal of Innate Immunity, 4 (4), 337–348. doi: 10.1159/000336619
Sharma, V., Hecker, N., Roscito, J. G., Foerster, L., Langer, B. E. & Hiller, M. (2018) A genomics approach reveals insights into the importance of gene losses for mammalian adaptations. Nature communications, 9 (1), 1215. doi: 10.1038/s41467-018-03667-1
Sharma, V., Lehmann, T., Stuckas, H., Funke, L., & Hiller, M. (2018). Loss of RXFP2 and INSL3 genes in Afrotheria shows that testicular descent is the ancestral condition in placental mammals. PLoS Biology, 16 (6), e2005293. doi: 10.1371/journal.pbio.2005293
Shen, B., Han, X., Jones, G., Rossiter, S. J., & Zhang, S. (2013). Adaptive Evolution of the Myo6 Gene in Old World Fruit Bats (Family: Pteropodidae). PLoS ONE, 8 (4), e62307. doi: 10.1371/journal.pone.0062307
Shen, B., Han, X., Zhang, J., Rossiter, S. J., & Zhang, S. (2012). Adaptive evolution in the glucose transporter 4 gene Slc2a4 in old world fruit bats (family: Pteropodidae). PLoS ONE, 7 (4), e33197. doi: 10.1371/journal.pone.0033197
Shultz, A. J., & Sackton, T. B. (2019). Immune genes are hotspots of shared positive selection across birds and mammals. ELife, 8,e41815. doi: 10.7554/eLife.41815
Simmons, N. B., Seymour, K. L., Habersetzer, J., & Gunnell, G. F. (2008). Primitive Early Eocene bat from Wyoming and the evolution of flight and echolocation. Nature, 451 (7180), 818-821. doi: 10.1038/nature06549
Sironi, M., Cagliani, R., Forni, D., & Clerici, M. (2015). Evolutionary insights into host-pathogen interactions from mammalian sequence data.Nature Reviews Genetics, 16 (4), 224-236. doi: 10.1038/nrg3905
Smit, A. F. A., Hubley, R. M., & Green, P. (n.d.). RepeatMasker. Retrieved from: http://Repeatmasker.Org.
Smith, M. D., Wertheim, J. O., Weaver, S., Murrell, B., Scheffler, K., & Kosakovsky Pond, S. L. (2015). Less is more: An adaptive branch-site random effects model for efficient detection of episodic diversifying selection. Molecular Biology and Evolution, 32 (5), 1342-1353. doi: 10.1093/molbev/msv022
Stamatakis, A. (2014). RAxML version 8: A tool for phylogenetic analysis and post-analysis of large phylogenies. Bioinformatics (Oxford, England), 30 (9), 1312-1313. doi: 10.1093/bioinformatics/btu033
Stanke, M., & Waack, S. (2003). Gene prediction with a hidden Markov model and a new intron submodel. Bioinformatics (Oxford, England), 19, 215-225. doi: 10.1093/bioinformatics/btg1080
Stolberg, V. R., Martin, B., Mancuso, P., Olszewski, M. A., Freeman, C. M., Curtis, J. L., & Chensue, S. W. (2014). Role of CC chemokine receptor 4 in natural killer cell activation during acute cigarette smoke exposure. The American Journal of Pathology, 184 (2), 454-463. doi: 10.1016/j.ajpath.2013.10.017
Storch, G., Sigé, B., & Habersetzer, J. (2002). Tachypteron franzeni n. gen., n. sp., earliest emballonurid bat from the Middle Eocene of Messel (Mammalia, Chiroptera). Paläontologische Zeitschrift, 79 (189-199). doi: 10.1007/bf02989856
Subudhi, A., Rapin, N., & Misra, V. (2019). Immune system modulation and viral persistence in bats: Understanding viral spillover.Viruses, 11 (2), 192 .doi: 10.3390/v11020192
Suyama, M., Torrents, D., & Bork, P. (2006). PAL2NAL: Robust conversion of protein sequence alignments into the corresponding codon alignments.Nucleic Acids Research, 34, 609-612. doi: 10.1093/nar/gkl315
Takada, A., Yoshida, S., Kajikawa, M., Miyatake, Y., Tomaru, U., Sakai, M., … Kasahara, M. (2008). Two Novel NKG2D Ligands of the Mouse H60 Family with Differential Expression Patterns and Binding Affinities to NKG2D. Journal of immunology (Baltimore, Md. : 1950), 180 (3), 1678–1685. doi: 10.4049/jimmunol.180.3.1678
Teeling, E. C., Vernes, S. C., Dávalos, L. M., Ray, D. A., Gilbert, M. T. P., & Myers, E. (2018). Bat Biology, Genomes, and the Bat1K Project: To Generate Chromosome-Level Genomes for All Living Bat Species.Annual Review of Animal Biosciences, 6, 23-46. doi: 10.1146/annurev-animal-022516-022811
Towner, J. S., Pourrut, X., Albariño, C. G., Nkogue, C. N., Bird, B. H., Grard, G., … Leroy, E. M. (2007). Marburg virus infection detected in a common African bat. PLoS ONE, 2 (8), e764. doi: 10.1371/journal.pone.0000764
Tsagkogeorga, G., Müller, S., Dessimoz, C., & Rossiter, S. J. (2017). Comparative genomics reveals contraction in olfactory receptor genes in bats. Scientific Reports, 7 (1), 259. doi: 10.1038/s41598-017-00132-9
Van Oosterhout, C. (2009). A new theory of MHC evolution: Beyond selection on the immune genes. Proceedings of the Royal Society B: Biological Sciences, 276 (1657), 657-665. doi: 10.1098/rspb.2008.1299
Vosseberg, J., Hoof, J. E., Marcet-Hoube, M. Vlimmeren, A., Wijk, T. G., & Snel B. (2020). Timing the origin of eukaryotic cellular complexity with ancient duplications. Nature Ecology & Evolution, 5,92-100. doi:10.1038/s41559-020-01320-z
Wang, K., Tian, S., Galindo-González, J., Dávalos, L. M., Zhang, Y., & Zhao, H. (2020). Molecular adaptation and convergent evolution of frugivory in Old World and neotropical fruit bats. Molecular Ecology, 29 (22), 4366–4381. doi: 10.1111/mec.15542
Wang, P., Luo, Y., Huang, J., Gao, S., Zhu, G.,Dang, Z., … Chen Y. (2020). The genome evolution and domestication of tropical fruit mango. Genome Biology, 21 (1), 60.doi.org/10.1186/s13059-020-01959-8
Welch, K. C., Herrera, M. L. G., & Suarez, R. K. (2008). Dietary sugar as a direct fuel for flight in the nectarivorous bat Glossophaga soricina . Journal of Experimental Biology, 211, 310-316. doi: 10.1242/jeb.012252
Wiens, M. E., Wilson, S. S., Lucero, C. M., & Smith, J. G. (2014). Defensins and Viral Infection: Dispelling Common Misconceptions.PLoS Pathogens, 10 (7), e1004186. doi: 10.1371/journal.ppat.1004186
Wilkinson, G. S., & Adams, D. M. (2019). Recurrent evolution of extreme longevity in bats. Biology Letters, 15 (4), 20180860. doi: 10.1098/rsbl.2018.0860
Wortham, B. W., Eppert, B. L., Motz, G. T., Flury, J. L., Orozco-Levi, M., Hoebe, K., … Borchers, M. T. (2012). NKG2D Mediates NK Cell Hyperresponsiveness and Influenza-Induced Pathologies in a Mouse Model of Chronic Obstructive Pulmonary Disease. Journal of immunology (Baltimore, Md. : 1950), 188 (9), 4468–4475. doi: 10.4049/jimmunol.1102643
Xie, J., Li, Y., Shen, X., Goh, G., Zhu, Y., Cui, J., … Zhou, P. (2018). Dampened STING-Dependent Interferon Activation in Bats.Cell Host and Microbe, 23 (3), 294-301. doi: 10.1016/j.chom.2018.01.006
Xu, D., & Lu, W. (2020). Defensins: A Double-Edged Sword in Host Immunity. Frontiers in Immunology , 11 (764), 1–9. doi: 10.3389/fimmu.2020.00764
Yang, Z. (2007). PAML 4: Phylogenetic analysis by maximum likelihood.Molecular Biology and Evolution, 24 (8), 1586–1591. doi: 10.1093/molbev/msm088
Yang, Z., Wong, W. S. W., & Nielsen, R. (2005). Bayes empirical Bayes inference of amino acid sites under positive selection. Molecular Biology and Evolution, 22 (4), 1107-1118. doi: 10.1093/molbev/msi097
Yates, A. D., Achuthan P., Akanni, W., Allen, J., Alvares, J. J., … Flicek, P. (2020). Ensembl 2020. Nucleic Acids Research, 48 (D1), D682-D688. doi:10.1093/nar/gkz966
Yohe, L. R., Devanna, P. Davies, K. T. J., Potter, J. H. T., Rossiter, S. J., Teeling, E. C., …, Dávalos L. M. (2019). Tissue Collection of Bats for –Omics Analyses and Primary Cell Culture. Journal of Visualized Experiments:JoVE, (152). doi: 10.3791/59505
You, X., Bian, C., Zan, Q., Xu, X., Liu, X., Chen, J., … Shi, Q. (2014). Mudskipper genomes provide insights into the terrestrial adaptation of amphibious fishes. Nature Communications, 5 , 5594. doi: 10.1038/ncomms6594
Yu, G., Smith, D. K., Zhu, H., Guan, Y., & Lam, T. T. Y. (2017). ggtree: an r package for visualization and annotation of phylogenetic trees with their covariates and other associated data. Methods in Ecology and Evolution, 8 (1), 28-36. doi: 10.1111/2041-210X.12628
Zafirova, B., Mandarić, S., Antulov, R., Krmpotić, A., Jonsson, H., Yokoyama, W. M., … Polić, B. (2009). Altered NK Cell Development and Enhanced NK Cell-Mediated Resistance to Mouse Cytomegalovirus in NKG2D-Deficient Mice. Immunity 31 (2), 270-282. doi: 10.1016/j.immuni.2009.06.017
Zepeda Mendoza, M. L., Xiong, Z., Escalera-Zamudio, M., Runge, A. K., Thézé, J., Streicker, D., … Gilbert, M. P. T. (2018). Hologenomic adaptations underlying the evolution of sanguivory in the common vampire bat. Nature Ecology and Evolution, 2 (4), 659-668. doi: 10.1038/s41559-018-0476-8
Zhang, G., Cowled, C., Shi, Z., Huang, Z., Bishop-Lilly, K. A., Fang, X., … Wang, J. (2013). Comparative analysis of bat genomes provides insight into the evolution of flight and immunity.Science, 339 (6118), 456-460. doi: 10.1126/science.1230835
Zhang, J., Nielsen, R., & Yang, Z. (2005). Evaluation of an improved branch-site likelihood method for detecting positive selection at the molecular level. Molecular Biology and Evolution, 22 (12), 2472-2479. doi: 10.1093/molbev/msi237
Zheng, D., Liwinski, T., & Elinav, E. (2020). Inflammasome activation and regulation: toward a better understanding of complex mechanisms.Cell Discovery, 6, 36. doi: 10.1038/s41421-020-0167-x
Zhi, L., Mans, J., Paskow, M. J., Brown, P. H., Schuck, P., Jonjić, S., … Margulies, D. H. (2010). Direct interaction of the mouse cytomegalovirus m152/gp40 immunoevasin with RAE-1 isoforms.Biochemistry, 49 (11), 2443-2453. doi: 10.1021/bi902130j
Zhou, P. (2020). Immune (Adaptive) Response in Bats. In Corrales-Aguilar, E & Schwemmle, M. (Eds.), Bats and Viruses: Current Research and Future Trends (pp. 135–148). Caister Academic Press. doi: 10.21775/9781912530144.09
Zhou, X., Dou, Q., Fan, G., Zhang, Q., Sanderford, M., Kaya, A., … Gladyshev, V. N. (2020). Beaver and Naked Mole Rat Genomes Reveal Common Paths to Longevity. Cell Reports, 32 (4), 107949. doi: 10.1016/j.celrep.2020.107949
Zimin, A. V., Marçais, G., Puiu, D., Roberts, M., Salzberg, S. L., & Yorke, J. A. (2013). The MaSuRCA genome assembler. Bioinformatics (Oxford, England), 29 (21), 2669-2677. doi: 10.1093/bioinformatics/btt476