References
Abe, S., Katagiri, T., Saito-Hisaminato, A., Usami, S., Inoue, Y., Tsunoda, T., & Nakamura, Y., (2003). Identification of CRYM as a candidate responsible for nonsyndromic deafness, through cDNA microarray analysis of human cochlear and vestibular tissues. American Journal of Human Genetics, 72 , 73-82.
Au, W., & Simmons, J. A., (2007). Echolocation in dolphins and bats. Physics Today , 60 , 40-45.
Benjamini, Y. & Hochberg, Y., (1995). Controlling the false discovery rate: a practical and powerful approach to multiple testing. Journal of the Royal Statistical Society ,57 , 289-300.
Clark, A. G., Eisen, M. B., Smith, D. R., Bergman, C. M., Oliver, B., Markow, T. A., Kaufman, T. C., Kellis, M., Gelbart, W., & Iyer, V. N., (2007). Evolution of genes and genomes on the Drosophila phylogeny. Nature , 450 , 203-218.
Darwin, C. R., (1859). On the origin of species by the means of natural selection. John Murray, London.
Davies, K. T. J., Cotton, J. A., Kirwan, J. D., Teeling, E. C., & Rossiter, S. J., (2012). Parallel signatures of sequence evolution among hearing genes in echolocating mammals: An emerging model of genetic convergence. Heredity ,108 , 480-489.
Dechmann, D. K. N., & Safi, K., (2009). Comparative studies of brain evolution: A critical insight from the Chiroptera. Biological Reviews of the Cambridge Philosophical Society , 84 , 161-172.
Dong, D., Lei, M., Hua, P., Pan, Y. H., Mu, S., Zheng, G., Pang, E., Lin, K., & Zhang, S., (2016). The genomes of two bat species with long constant frequency echolocation calls. Molecular Biology and Evolution , 34 , 20-34.
Dong, D., Lei, M., Liu, Y., & Zhang, S., (2013). Comparative inner ear transcriptome analysis between the Rickett’s big-footed bats (Myotis ricketti ) and the greater short-nosed fruit bats (Cynopterus sphinx ). BMC Genomics ,14 , 916.
Edgar, R. C., (2004). MUSCLE: Multiple sequence alignment with high accuracy and high throughput.Nucleic Acids Research , 32 , 1792-1797.
Feldmeyer, B., Greshake, B., Funke, E., Ebersberger, I., & Pfenninger, M., (2015). Positive selection in development and growth rate regulation genes involved in species divergence of the genus Radix . BMC Evolutionary Biology ,15 , 164.
Grabherr, M. G., Haas, B. J., Yassour, M., Levin, J. Z., Thompson, D. A., Amit, I., Adiconis, X., Fan, L., Raychowdhury, R., & Zeng, Q., (2011). Full-length transcriptome assembly from RNA-Seq data without a reference genome. Nature Biotechnology , 29 , 644-652.
Guindon, S., Dufayard, J. F., Lefort, V., Anisimova, M., Hordijk, W., & Gascuel, O., (2010). New algorithms and methods to estimate maximum-likelihood phylogenies: assessing the performance of PhyML 3.0. Systematic Biology , 59 , 307-321.
Guo, C., Cho, K. S., Li, Y., Tchedre, K., Antolik, C., Ma, J., Chew, J., Utheim, T. P., Huang, X. A., Yu, H., Malik, M. T. A., Anzak, N., & Chen, D. F., (2018). IGFBPL1 Regulates Axon Growth through IGF-1-mediated Signaling Cascades. Scientific Reports , 8 , 2054.
Hao, Y., Xiong, Y., Cheng, Y., Song, G., Jia, C., Qu, Y., & Lei, F., (2019). Comparative transcriptomics of 3 high-altitude passerine birds and their low-altitude relatives.Proceedings of the National Academy of Sciences , 116 , 11851-11856.
Harvey, P. H., & Krebs, J. R., (1990). Comparing Brains. Science , 249 , 140-146.
Hong, I., Kang, T., Yun, K.N., Yoo, Y., Park, S., Kim, J., An, B., Song, S., Lee, S., Kim, J., Song, B., Kwon, K. H., Kim, J. Y., Park, Y. M., & Choi, S., (2013). Quantitative proteomics of auditory fear conditioning. Biochemical and Biophysical Research Communications , 434 , 87-94.
Hosoya, M., Fujioka, M., Ogawa, K., & Okano, H., (2016). Distinct expression patterns of causative genes responsible for hereditary progressive hearing loss in non-human primate cochlea. Scientific Reports , 6 , 22250.
Hughes, J. F., Skaletsky, H., Pyntikova, T., Graves, T. A., van Daalen, S. K. M., Minx, P. J., Fulton, R. S., McGrath, S. D., Locke, D. P., & Friedman, C., (2010). Chimpanzee and human Y chromosomes are remarkably divergent in structure and gene content. Nature , 463 , 536-539.
Iseli, C., Jongeneel, C. V., & Bucher, P., (1999). ESTScan: a program for detecting, evaluating, and reconstructing potential coding regions in EST sequences.International Conference on Intelligent Systems for Molecular Biology , 138-148.
Jones, G., & Teeling, E. C., (2006). The evolution of echolocation in bats. Trends in Ecology and Evolution , 21 , 150-156.
Joo, A., Long, R., Cheng, Z., Alexander, C., Chang, W., & Klein, O. D., (2016). Sprouty2 regulates endochondral bone formation by modulation of RTK and BMP signaling.Bone , S8756328216301107.
Kirwan, J. D., Bekaert, M., Commins, J. M., Davies, K. T. J., Rossiter, S. J., & Teeling, E. C., (2013). A phylomedicine approach to understanding the evolution of auditory sensory perception and disease in mammals. Evolutionary Applications , 6 , 412-422.
Koenig, D., Jimenez-Gomez, J. M., Kimura, S., Fulop, D., Chitwood, D.H ., Headland, L. R., Kumar, R., Covington, M. F., Devisetty, U. K., Tat, A. V., Tohge, T., Bolger, A., Schneeberger, K., Ossowski, S., Lanz, C., Xiong, G., Taylor-Teeples, M., Brady, S. M., Pauly, M., Weigel, D., Usadel, B., Fernie, A. R., Peng, J., Sinha, N. R., & Maloof, J. N., (2013). Comparative transcriptomics reveals patterns of selection in domesticated and wild tomato.Proceedings of the National Academy of Sciences of the United States of America , 110 , E2655-2662.
Lemmon, E.M., & Lemmon, A.R., (2013). High-throughput genomic data in systematics and phylogenetics.Annual Review of Ecology, Evolution, and Systematics , 44 , 99-121.
Li, G., Wang, J., Rossiter, S. J., Jones, G., Cotton, J. A., & Zhang, S., (2008). The hearing gene Prestin reunites echolocating bats. Proceedings of the National Academy of Sciences of the United States of America , 105 , 13959-13964.
Li, J., Sun, K., Dai, W., Leng, H., & Feng, J., (2022a). Divergence in interspecific and intersubspecific gene expression between two closely related horseshoe bats (Rhinolophus ). Journal of Mammalogy , 104 , 62-75.
Li, J., Sun, K., Dai, W., Leng, H., Li, A., & Feng, J., (2022b). Extensive adaptive variation in gene expression within and between closely related horseshoe bats (Chiroptera, Rhinolophus ) Revealed by Three Organs.Animals , 12 .
Li, L., (2003). OrthoMCL_ Identification of ortholog groups for eukaryotic genomes. Genome Research , 13 , 2178-2189.
Li, Y., Liu, Z., Shi, P., & Zhang, J., (2010). The hearing gene Prestin unites echolocating bats and whales. Current Biology , 20 , R55-56.
Liu, T., Sun, K., Csorba, G., Zhang, K., Zhang, L., Zhao, H., Jin, L., Thong, V. D., Xiao, Y., & Feng, J., (2019). Species delimitation and evolutionary reconstruction within an integrative taxonomic framework: A case study on Rhinolophus macrotis complex (Chiroptera: Rhinolophidae). Molecular Phylogenetics and Evolution , 139 , 106544.
Liu, Y., Han, N., Franchini, L.F., Xu, H. H., Pisciottano, F., B., Elgoyhen, A. B., Rajan, K. E., & Zhang, S., (2012). The voltage-gated potassium channel subfamily KQT member 4 (KCNQ4) displays parallel evolution in echolocating bats. Molecular Biology and Evolution ,29 , 1441-1450.
Liu, Z., Li, S. D., Wang, W., Xu, D. M., Murphy, R. W., & Shi, P., (2011). Parallel evolution of KCNQ4 in echolocating bats. PLoS ONE , 6 , 6:e26618.
Ma, J., Zhang, L., Shen, F., Geng, Y., Huang, Y., Wu, H., Fan, Z., Hou, R., Song, Z., Yue, B., & Zhang, X., (2023). Gene expressions between obligate bamboo-eating pandas and non-herbivorous mammals reveal converged specialized bamboo diet adaptation. BMC Genomics , 24 , 23.
Marianne, Cynthia, Thomas, & Jeanette, (2004). Echolocation in Bats and Dolphins. Chicago University P.
Marie Curie, S. N., Butlin, R., Debelle, A., Kerth, C., Snook, R. R., Beukeboom, L. W., Castillo Cajas, R. F., Diao, W., Maan, M. E., Paolucci, S., Weissing, F. J., van de Zande, L., Hoikkala, A., Geuverink, E., Jennings, J., Kankare, M., Knott, K. E., Tyukmaeva, V. I., Zoumadakis, C., Ritchie, M. G., Barker, D., Immonen, E., Kirkpatrick, M., Noor, M., Macias Garcia, C., Schmitt, T., & Schilthuizen, M., (2012). What do we need to know about speciation? Trends in Ecology and Evolution , 27 , 27-39.
Marra, N. J., Romero, A., & DeWoody, J. A., (2014). Natural selection and the genetic basis of osmoregulation in heteromyid rodents as revealed by RNA-seq. Molecular Ecology ,23 , 2699-2711.
Mason, N. A., & Taylor, S. A., (2015). Differentially expressed genes match bill morphology and plumage despite largely undifferentiated genomes in a Holarctic songbird.Molecular Ecology , 24 , 3009-3025.
Mccormack, J. E., Hird, S. M., Zellmer, A. J., Carstens, B. C., & Brumfield, R. T., (2013). Applications of next-generation sequencing to phylogeography and phylogenetics. Molecular Phylogenetics and Evolution , 66 , 526-538.
Mitterboeck, T. F., Liu, S., Adamowicz, S. J., Fu, J., Zhang, R., Song, W., Meusemann, K., & Zhou, X., (2017). Positive and relaxed selection associated with flight evolution and loss in insect transcriptomes. GigaScience ,6 , 1-14.
Morandin, C., Tin, M. M., Abril, S., Gomez, C., Pontieri, L., Schiott, M., Sundstrom, L., Tsuji, K., Pedersen, J. S., Helantera, H., & Mikheyev, A. S., (2016). Comparative transcriptomics reveals the conserved building blocks involved in parallel evolution of diverse phenotypic traits in ants. Genome Biology and Evolution , 17 , 43.
Murga-Zamalloa, C. A., Atkins, S. J., Peranen, J., Swaroop, A., & Khanna, H., (2010). Interaction of retinitis pigmentosa GTPase regulator (RPGR) with RAB8A GTPase: implications for cilia dysfunction and photoreceptor degeneration.Human Molecular Genetics , 19 , 3591-3598.
Naumenko, S. A., Logacheva, M. D., Popova, N. V., Klepikova, A. V., Penin, A. A., Bazykin, G. A., Etingova, A. E., Mugue, N. S., Kondrashov, A. S., & Yampolsky, L. Y., (2017). Transcriptome-based phylogeny of endemic Lake Baikal amphipod species flock: fast speciation accompanied by frequent episodes of positive selection. Molecular Ecology , 26 , 536-553.
O’Callaghan, B., Bosch, A. M., & Houlden, H., (2019). An update on the genetics, clinical presentation, and pathomechanisms of human riboflavin transporter deficiency.Journal of Inherited Metabolic Disease , 42 , 598-607.
Pangrsic, T., & Vogl, C., (2018). Balancing presynaptic release and endocytic membrane retrieval at hair cell ribbon synapses. Febs Letters , 592 , 3633-3650.
Pespeni, M.H., Ladner, J. T., & Moczek, A. P., (2017). Signals of selection in conditionally expressed genes in the diversification of three horned beetle species.Journal of Evolutionary Biology , 30 , 1644-1657.
Sanchez-Calderon, H., Rodriguez-de la Rosa, L., Milo, M., Pichel, J.G., Holley, M., & Varela-Nieto, I., (2010). RNA microarray analysis in prenatal mouse cochlea reveals novel IGF-I target genes: implication of MEF2 and FOXM1 transcription factors.PLoS ONE , 5 , e8699.
Shao, Y., Li, J. X., Ge, R. L., Zhong, L., Irwin, D. M., Murphy, R. W., & Zhang, Y. P., (2015). Genetic adaptations of the plateau zokor in high-elevation burrows.Scientific Reports , 5 , 17262.
Sharma, T. P., Wiley, L. A., Whitmore, S. S., Anfinson, K. R., Cranston, C. M., Oppedal, D. J., Daggett, H. T., Mullins, R. F., Tucker, B. A., & Stone, E. M., (2017). Patient-specific induced pluripotent stem cells to evaluate the pathophysiology of TRNT1-associated Retinitis pigmentosa. Stem Cell Research , 21 , 58-70.
Shen, Y., Liang, L., Zhu, Z., Zhou, W., Irwin, D. M., & Zhang, Y., (2010). Adaptive evolution of energy metabolism genes and the origin of flight in bats. Proceedings of the National Academy of Sciences of the United States of America ,107 , 8666-8671.
Soskine, M., & Tawfik, D. S., (2010). Mutational effects and the evolution of new protein functions.Nature Reviews Genetics , 11 , 572-582.
Sun, G., Yu, H., Wang, P., Lopez-Guerrero, M., Mural, R. V., Mizero, O. N., Grzybowski, M., Song, B., van Dijk, K., Schachtman, D. P., Zhang, C., & Schnable, J. C., (2023). A role for heritable transcriptomic variation in maize adaptation to temperate environments. Genome Biology , 24 , 55.
Tian, R., Yin, D., Liu, Y., Seim, I., Xu, S., & Yang, G., (2017). Adaptive evolution of energy metabolism-related genes in hypoxia-tolerant mammals. Frontiers in Genetics , 8 , 205.
Wang, H., Zhao, H., Sun, K., Huang, X., Jin, L., & Feng, J., (2019). Evolutionary basis of high-frequency hearing in the cochleae of echolocators revealed by comparative genomics. Genome Biology and Evolution , 12 , 3740-3753.
Wei, L., Ding, D., & Salvi, R., (2010). Salicylate-induced degeneration of cochlea spiral ganglion neurons-apoptosis signaling. Neuroscience , 168 , 288-299.
Wright, K.D., Mahoney R. A. A., Zhang, J., & Shim, K., (2015). Cooperative and independent functions of FGF and Wnt signaling during early inner ear development. BMC Developmental Biology , 15 , 33.
Wu, H., Jiang, T. L., Müller, R., & Feng, J., (2015). The allometry of echolocation call frequencies in horseshoe bats: nasal capsule and pinna size are the better predictors than forearm length. Journal of Zoology , 297 , 211-219.
Yang, Z., (2007). PAML 4: phylogenetic analysis by maximum likelihood. Molecular Biology and Evolution , 24 , 1586-1591.
Yang, Z., Wong, W. S. W., & Rasmus, N., (2005). Bayes empirical bayes inference of amino acid sites under positive selection. Molecular Biology & Evolution , 22 , 1107-1118.
Ying, H., Garrison, J. E., Grace, K., Schmitz, A. C., Searby C. C., QH, Z., Datta, P., Nishimura, D., Seo, S., & Sheffidld, V., (2017). ARRDC3 sponge transgenic mouse model reveals important roles for the microRNA-183 (miR-183)/96/182 cluster in postmitotic photoreceptors of the retina. PLoS Genetics , 13 , e1007057.
Ying, H., Janelle, E. G., Gunhee, K., Addison, R. S., Charles, C. S., Qihong. Z., Poppy, D., Darryl, Y. N., Seongjin, S., & Val, C. S. (2017). BBSome function is required for both the morphogenesis and maintenance of the photoreceptor outer segment.PLoS Genetics , 13 , e1007057.
Young, M. D., Wakefield, M. J., Smyth, G. K., & Oshlack, A., (2010). Gene ontology analysis for RNA-seq: accounting for selection bias. Genome Biology ,11 , R14.
Yousaf, R., Ahmed, Z. M., Giese, A. P., Morell, R. J., Lagziel, A., Dabdoub, A., Wilcox, E. R., Riazuddin, S., Friedman, T. B., & Riazuddin, S., (2018). Modifier variant of METTL13 suppresses human GAB1-associated profound deafness. The Journal of clinical investigation , 128 , 1509-1522.
Yu, X., Wei, P., Zhao, S., Chen, Z., Li, X., Zhang, W., Liu, C., Yang, Y., Li, X., & Liu, X., (2023). Population transcriptomics uncover the relative roles of positive selection and differential expression in Batrachium bungeiadaptation to the Qinghai-Tibetan plateau. Plant Cell Reports ,42 , 879-893.
Zhang, L., Jones, G., Zhang, J., Zhu, G., Parsons, S., Rossiter, S. J., & Zhang, S., (2009). Recent surveys of bats (Mammalia: Chiroptera) from China. I. Rhinolophidae and Hipposideridae. Acta Chiropterologica , 11 , 71-88.
Zhang, L., Sun, K., Csorba, G., Hughes, A. C., Jin, L., Xiao, Y., & Feng, J., (2021). Complete mitochondrial genomes reveal robust phylogenetic signals and evidence of positive selection in horseshoe bats. BMC Ecology and Evolution ,21 , 199.
Zhang, L., Sun, K., Liu, T., Zhao, H., Csorba, G., Jin, L., Thong, V. D., & Feng, J., (2018). Multilocus phylogeny and species delimitation within the philippinensisgroup (Chiroptera: Rhinolophidae). Zoologica Scripta , 47 , 655-672.
Zhao, H., Wang, H., Liu, T., Liu, S., Jin, L., Huang, X., Dai, W., Sun, K., & Feng, J., (2019). Gene expression vs. sequence divergence: comparative transcriptome sequencing among natural Rhinolophus ferrumequinum populations with different acoustic phenotypes. Frontiers in Zoology , 16 , 37.