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.