References
Alexa, A., Rahnenführer, J. & Lengauer, T. 2006. Improved scoring of
functional groups from gene expression data by decorrelating GO graph
structure. Bioinformatics 22: 1600-1607.
Austin, S. & Nowikovsky, K. 2021. Mitochondrial osmoregulation in
evolution, cation transport and metabolism. Biochimica et Biophysica
Acta (BBA) - Bioenergetics 1862: 148368.
Bachman, P.M. & Rand, G.M. 2008. Effects of salinity on native
estuarine fish species in South Florida. Ecotoxicology 17: 591.
Batista, T.M., Dagdeviren, S., Carroll, S.H., Cai, W., Melnik, V.Y.,
Noh, H.L., Saengnipanthkul, S., Kim, J.K., Kahn, C.R. & Lee, R.T. 2020.
Arrestin domain-containing 3 (Arrdc3) modulates insulin action and
glucose metabolism in liver. Proceedings of the National Academy of
Sciences 117: 6733-6740.
Bell, M.A. & Foster, S.A. 1994. The evolutionary biology of the
threespine stickleback. New York: Oxford University Press.
Bell, M.A. & Richkind, K.E. 1981. Clinal variation of lateral plates in
threespine stickleback fish. American Naturalist 117: 113-132.
Boeuf, G. & Payan, P. 2001. How should salinity influence fish growth?
Comparative Biochemistry and Physiology C-Toxicology & Pharmacology
130: 411-423.
Bourgon, R., Gentleman, R. & Huber, W. 2010. Independent filtering
increases detection power for high-throughput experiments. Proceedings
of the National Academy of Sciences of the United States of America 107:
9546-9551.
Chevin, L.M., Lande, R. & Mace, G.M. 2010. Adaptation, plasticity, and
extinction in a changing environment: towards a predictive theory. PLoS
Biol 8: e1000357.
Chu, P., He, L., Zhu, D., Huang, R., Liao, L., Li, Y., Zhu, Z. & Wang,
Y. 2019. Identification, expression and functional characterisation of
CYP1A in grass carp (Ctenopharyngodon idella ). Fish Shellfish
Immunol 95: 35-43.
Colaneri, A.C., Tunc-Ozdemir, M., Huang, J.P. & Jones, A.M. 2014.
Growth attenuation under saline stress is mediated by the heterotrimeric
G protein complex. BMC Plant Biology 14: 129.
Cui, W., Ma, A., Huang, Z., Wang, X., Liu, Z., Xia, D., Yang, S. &
Zhao, T. 2020. Comparative transcriptomic analysis reveals mechanisms of
divergence in osmotic regulation of the turbot Scophthalmus
maximus . Fish Physiology and Biochemistry 46: 1519-1536.
Cutler, C.P., Martinez, A.-S. & Cramb, G. 2007. The role of aquaporin 3
in teleost fish. Comparative Biochemistry and Physiology Part A:
Molecular & Integrative Physiology 148: 82-91.
DeFaveri, J., Shikano, T., Shimada, Y., Goto, A. & Merilä, J. 2011.
Global analysis of genes involved in freshwater adation in threespine
sticklebacks (Gasterosteus aculeatus ) Evolution 65: 1800-1807.
DeFaveri, J., Shikano, T., Shimada, Y. & Merilä, J. 2013. High degree
of genetic differentiation in marine three-spined sticklebacks
(Gasterosteus aculeatus ). Molecular Ecology 22: 4811-4828.
Delgado, M.L. & Ruzzante, D.E. 2020. Investigating diadromy in fishes
and its loss in an -omics era. iScience 23: 101837.
Erickson, G.R., Alexopoulos, L.G. & Guilak, F. 2001. Hyper-osmotic
stress induces volume change and calcium transients in chondrocytes by
transmembrane, phospholipid, and G-protein pathways. J Biomech 34:
1527-35.
Ern, R., Huong, D.T.T., Cong, N.V., Bayley, M. & Wang, T. 2014. Effect
of salinity on oxygen consumption in fishes: a review. Journal of Fish
Biology 84: 1210-1220.
Evans, D.H., Piermarini, P.M. & Choe, K.P. 2005. The multifunctional
fish gill: dominant site of gas exchange, osmoregulation, acid-base
regulation, and excretion of nitrogenous waste. Physiological Reviews
85: 97-177.
Evans, T.G. 2015. Considerations for the use of transcriptomics in
identifying the ‘genes that matter’ for environmental adaptation.
Journal of Experimental Biology 218: 1925-1935.
Fiol, D.F. & Kültz, D. 2007. Osmotic stress sensing and signaling in
fishes. The FEBS Journal 274: 5790-5798.
Fiol, D.F., Sanmarti, E., Sacchi, R. & Kültz, D. 2009. A novel tilapia
prolactin receptor is functionally distinct from its paralog. Journal of
Experimental Biology 212: 2007-2015.
Gao, C.-H. 2019. ggVennDiagram: A ’ggplot2’ Implement of Venn Diagram. R
package version 0.3. https://CRAN.R-project.org/package=ggVennDiagram.
Ghalambor, C.K., Hoke, K.L., Ruell, E.W., Fischer, E.K., Reznick, D.N.
& Hughes, K.A. 2015. Non-adaptive plasticity potentiates rapid adaptive
evolution of gene expression in nature. Nature 525: 372-5.
Gibbons, T.C., Metzger, D.C.H., Healy, T.M. & Schulte, P.M. 2017. Gene
expression plasticity in response to salinity acclimation in threespine
stickleback ecotypes from different salinity habitats. Molecular Ecology
26: 2711-2725.
Gomez, D., Sunyer, J.O. & Salinas, I. 2013. The mucosal immune system
of fish: The evolution of tolerating commensals while fighting
pathogens. Fish & Shellfish Immunology 35: 1729-1739.
Grøtan, K., Østbye, K., Taugbøl, A. & Vøllestad, L.A. 2012. No
short-term effect of salinity on oxygen consumption in threespine
stickleback (Gasterosteus aculeatus) from fresh, brackish, and salt
water. Canadian Journal of Zoology 90: 1386-1393.
Guo, B., DeFaveri, J., Sotelo, G., Nair, A. & Merilä, J. 2015.
Population genomic evidence for adaptive differentiation in Baltic Sea
three-spined sticklebacks. BMC Biology 13: 19.
Habourdin, C., Klein, G., Araki, T., Williams, J.G. & Aubry, L. 2013.
The arrestin-domain containing protein AdcA is a response element to
stress. Cell Communication and Signaling 11: 91.
Hartmann, E., Rapoport, T.A. & Lodish, H.F. 1989. Predicting the
orientation of eukaryotic membrane-spanning proteins. Proceedings of the
National Academy of Sciences of the United States of America 86:
5786-5790.
Hasan, M.M., DeFaveri, J., Kuure, S., Dash, S.N., Lehtonen, S., Merilä,
J. & McCairns, R.J.S. 2017. Sticklebacks adapted to divergent osmotic
environments show differences in plasticity for kidney morphology and
candidate gene expression. The Journal of Experimental Biology 220:
2175-2186.
Havird, J.C., Meyer, E., Fujita, Y., Vaught, R.C., Henry, R.P. &
Santos, S.R. 2019. Disparate responses to salinity across species and
organizational levels in anchialine shrimps. The Journal of Experimental
Biology 222: jeb211920.
Hoar, W.S. & Randall, D.J. 1984. Fish Physiology. gills. ion and water
transfer. Orlando: Academic press,INC.
Hohenlohe, P.A., Bassham, S., Etter, P.D., Stiffler, N., Johnson, E.A.
& Cresko, W.A. 2010. Population genomics of parallel adaptation in
threespine stickleback using sequenced RAD tags. Plos Genetics 6.
Horng, J.-L., Lin, L.-Y., Huang, C.-J., Katoh, F., Kaneko, T. & Hwang,
P.-P. 2007. Knockdown of V-ATPase subunit A (atp6v1a) impairs acid
secretion and ion balance in zebrafish (Danio rerio ). American
Journal of Physiology-Regulatory, Integrative and Comparative Physiology
292: R2068-R2076.
Indrischek, H., Prohaska, S.J., Gurevich, V.V., Gurevich, E.V. &
Stadler, P.F. 2017. Uncovering missing pieces: duplication and deletion
history of arrestins in deuterostomes. BMC Evolutionary Biology 17: 163.
Jiang, J.-L., Xu, J., Ye, L., Sun, M.-L., Jiang, Z.-Q. & Mao, M.-G.
2020. Identification of differentially expressed genes in gills of tiger
puffer (Takifugu rubripes ) in response to low-salinity stress.
Comparative Biochemistry and Physiology Part B: Biochemistry and
Molecular Biology 243-244: 110437.
Jones, F.C., Chan, Y.F., Schmutz, J., Grimwood, J., Brady, S.D.,
Southwick, A.M., Absher, D.M., Myers, R.M., Reimchen, T.E., Deagle,
B.E., Schluter, D. & Kingsley, D.M. 2012a. A genome-wide SNP genotyping
array reveals patterns of global and repeated species-pair divergence in
sticklebacks. Current Biology 22: 83-90.
Jones, F.C., Grabherr, M.G., Chan, Y.F., Russell, P., Mauceli, E.,
Johnson, J., Swofford, R., Pirun, M., Zody, M.C., White, S., Birney, E.,
Searle, S., Schmutz, J., Grimwood, J., Dickson, M.C., Myers, R.M.,
Miller, C.T., Summers, B.R., Knecht, A.K., Brady, S.D., Zhang, H.L.,
Pollen, A.A., Howes, T., Amemiya, C., Lander, E.S., Di Palma, F.,
Lindblad-Toh, K., Broad Inst Genome Sequencing Platform, Whole Genome
Assembly Team & Kingsley, D.M. 2012b. The genomic basis of adaptive
evolution in threespine sticklebacks. Nature 484: 55-61.
Kato, G., Miyazawa, H., Nakayama, Y., Ikari, Y., Kondo, H., Yamaguchi,
T., Sano, M. & Fischer, U. 2018. A novel antigen-sampling cell in the
teleost gill epithelium with the potential for direct antigen
presentation in mucosal tissue. Frontiers in Immunology 9.
Klepaker, T. 1996. Lateral plate polymorphism in marine and estuarine
populations of the threespine stickleback (Gasterosteus
aculeatus ) along the coast of Norway. Copeia: 832-838.
Knag, A.C. & Taugbøl, A. 2013. Acute exposure to offshore produced
water has an effect on stress- and secondary stress responses in
three-spined stickleback Gasterosteus aculeatus . Comparative
Biochemistry and Physiology C-Toxicology & Pharmacology 158: 173-180.
Kumai, Y., Ward, M.A. & Perry, S.F. 2012. β-Adrenergic regulation of
Na+ uptake by larval zebrafish Danio rerio in acidic and ion-poor
environments. Am J Physiol Regul Integr Comp Physiol 303: R1031-41.
Lande, R. 1976. Natural selection and random genetic drift in phenotypic
evolution. Evolution 30: 314-334.
Lavado, R., Aparicio-Fabre, R. & Schlenk, D. 2014. Effects of salinity
acclimation on the expression and activity of Phase I enzymes (CYP450
and FMOs) in coho salmon (Oncorhynchus kisutch ). Fish Physiol
Biochem 40: 267-78.
Lefkowitz, R.J. & Shenoy, S.K. 2005. Transduction of receptor signals
by ß-arrestins. Science 308: 512-517.
Leguen, I., Odjo, N., Le Bras, Y., Luthringer, B., Baron, D., Monod, G.
& Prunet, P. 2010. Effect of seawater transfer on CYP1A gene expression
in rainbow trout gills. Comp Biochem Physiol A Mol Integr Physiol 156:
211-7.
Lenoir, C., Rollason, V., Desmeules, J.A. & Samer, C.F. 2021. Influence
of inflammation on cytochromes P450 activity in adults: a systematic
review of the literature. Frontiers in Pharmacology 12.
Lescak, E.A., Bassham, S.L., Catchen, J., Gelmond, O., Sherbick, M.L.,
von Hippel, F.A. & Cresko, W.A. 2015. Evolution of stickleback in 50
years on earthquake-uplifted islands. Proceedings of the National
Academy of Sciences of the United States of America 112: E7204-E7212.
Leung, C., Rescan, M., Grulois, D. & Chevin, L.-M. 2020. Reduced
phenotypic plasticity evolves in less predictable environments. Ecology
Letters 23: 1664-1672.
Levis, N.A. & Pfennig, D.W. 2016. Evaluating ‘plasticity-first’
evolution in nature: key criteria and empirical approaches. Trends in
Ecology & Evolution 31: 563-574.
Liu, W., Kang, L.F., Xu, Q., Tao, C.C., Yan, J. & Sang, T. 2019.
Increased expression diversity buffers the loss of adaptive potential
caused by reduction of genetic diversity in new unfavourable
environments. Biology Letters 15.
Lizarbe, M.A., Barrasa, J.I., Olmo, N., Gavilanes, F. & Turnay, J.
2013. Annexin-phospholipid interactions. Functional implications.
International journal of molecular sciences 14: 2652-2683.
Lv, J., Liu, P., Gao, B. & Li, J. 2016. The identification and
characteristics of salinity-related microRNAs in gills of Portunus
trituberculatus . Cell stress & chaperones 21: 63-74.
Mäkinen, H., Papakostas, S., Vøllestad, L.A., Leder, E.H. & Primmer,
C.R. 2016. Plastic and evolutionary gene expression responses are
correlated in European grayling (Thymallus thymallus )
subpopulations adapted to different thermal environments. Journal of
Heredity 107: 82-89.
Mazzarella, A.B., Voje, K.L., Hansson, T.H., Taugbøl, A. & Fischer, B.
2015. Strong and parallel salinity-induced phenotypic plasticity in one
generation of threespine stickleback. Journal of Evolutionary Biology
28: 667-677.
McCairns, R.J.S. & Bernatchez, L. 2010. Adaptive divergence between
freshwater and marine sticklebacks: Insights into the role of phenotypic
plasticity from an intergrated analysis of candidate gene expression.
Evolution 64: 1029-1047.
McCormick, S.D., Farrell, A.P. & Brauner, C.J. 2012. Euryhaline fishes.
594 pp.
Møller, J.J. 2003. Relative sea level change in Fennoscandia. Net
version 3.00. University of Tromsø: Department of Geology, TMU.
Mommsen, T.P. 1984. Metabolism of the gill. In: Hoar, W.S. & Randall,
D.J., eds. Fish Physiology. Gills. Ion and water transfer. Orlando:
Academic press,INC, pp. 203-238.
Morris, M.R.J., Richard, R., Leder, E.H., Barrett, R.D.H., Aubin-Horth,
N. & Rogers, S.M. 2014. Gene expression plasticity evolves in response
to colonization of freshwater lakes in threespine stickleback. Molecular
Ecology 23: 3226-3240.
Mustelin, T., Vang, T. & Bottini, N. 2005. Protein tyrosine
phosphatases and the immune response. Nature Reviews Immunology 5:
43-57.
Papakostas, S., Vøllestad, L.A., Bruneaux, M., Aykanat, T., Vanoverbeke,
J., Ning, M., Primmer, C.R. & Leder, E.H. 2014. Gene pleiotropy
constrains gene expression changes in fish adapted to different thermal
conditions. Nature Communications 5: 4071.
Perry, S.F. 1997. The chloride cell: structure and function in the gills
of freshwater fishes. Annual Review of Physiology 59: 325-347.
Pertl, H., Pockl, M., Blaschke, C. & Obermeyer, G. 2010. Osmoregulation
in Lilium pollen grains occurs via modulation of the plasma membrane
H+ ATPase activity by 14-3-3 proteins. Plant
Physiology 154: 1921-1928.
Pickford, G.E. & Phillips, J.G. 1959. Prolactin, a factor in promoting
survival of hypophysectomized killifish in fresh water. Science 130:
454-455.
Pigliucci, M. 2001. Phenotypic plasticity: beyond nature and nurture.
Baltimore: Johns Hopkins University Press
R Development Core Team. 2020. R: a language and environment for
statistical computing. Vienna, Austria: R foundation for statistical
computing, pp. Retrieved from http://www.R-project.org.
Rankin, J.C. & Jensen, F.B. 1993. Fish ecophysiology. London:
SpringerLink.
Rastorguev, S.M., Nedoluzhko, A.V., Gruzdeva, N.M., Boulygina, E.S.,
Tsygankova, S.V., Oshchepkov, D.Y., Mazur, A.M., Prokhortchouk, E.B. &
Skryabin, K.G. 2018. Gene expression in the three-spined stickleback
(Gasterosteus aculeatus ) of marine and freshwater ecotypes. Acta
naturae 10: 66-74.
Roberge, C., Normandeau, E., Einum, S., Guderley, H. & Bernatchez, L.
2008. Genetic consequences of interbreeding between farmed and wild
Atlantic salmon: insights from the transcriptome. Molecular Ecology 17:
314-324.
Robinson, M.D., McCarthy, D.J. & Smyth, G.K. 2010. edgeR: a
Bioconductor package for differential expression analysis of digital
gene expression data. Bioinformatics 26: 139-140.
Robinson, M.D. & Oshlack, A. 2010. A scaling normalization method for
differential expression analysis of RNA-seq data. Genome Biology 11.
Robinson, M.D. & Smyth, G.K. 2007. Moderated statistical tests for
assessing differences in tag abundance. Bioinformatics 23: 2881-2887.
Sangiao-Alvarellos, S., Arjona, F.J., del Río, M.P.M., Míguez, J.M.,
Mancera, J.M. & Soengas, J.L. 2005. Time course of osmoregulatory and
metabolic changes during osmotic acclimation in Sparus auratus .
Journal of Experimental Biology 208: 4291-4304.
Sangiao-Alvarellos, S., Laiz-Carrión, R., Guzmán, J.M., Río, M.P.M.d.,
Miguez, J.M., Mancera, J.M. & Soengas, J.L. 2003. Acclimation ofS. aurata to various salinities alters energy metabolism of
osmoregulatory and nonosmoregulatory organs. American Journal of
Physiology-Regulatory, Integrative and Comparative Physiology 285:
R897-R907.
Schultz, E.T. & McCormick, S.D. 2012. Euryhalinity in an evolutionary
context. In: Stephen D. McCormick, A.P.F. & Colin, J.B., eds. Fish
physiology. Academic Press, pp. 477-533.
Shaughnessy, C.A. & McCormick, S.D. 2020. Functional characterization
and osmoregulatory role of the
Na+-K+-2Cl−cotransporter in the gill of sea lamprey (Petromyzon marinus ), a
basal vertebrate. American Journal of Physiology-Regulatory, Integrative
and Comparative Physiology 318: R17-R29.
Shimada, Y., Shikano, T. & Merilä, J. 2011. A high incidence of
selection on physiologically important genes in the three-spined
stickleback, Gasterosteus aculeatus . Molecular Biology and
Evolution 28: 181-193.
Sih, A., Ferrari, M.C. & Harris, D.J. 2011. Evolution and behavioural
responses to human-induced rapid environmental change. Evol Appl 4:
367-87.
Song, J.-Y., Casanova-Nakayama, A., Möller, A.-M., Kitamura, S.-I.,
Nakayama, K. & Segner, H. 2020. Aryl hydrocarbon receptor signaling is
functional in immune cells of rainbow trout (Oncorhynchus
mykiss ). International journal of molecular sciences 21: 6323.
Sun-Wada, G.H., Wada, Y. & Futai, M. 2004. Diverse and essential roles
of mammalian vacuolar-type proton pump ATPase: toward the physiological
understanding of inside acidic compartments. Biochim Biophys Acta 1658:
106-14.
Svensson, E.I., Gomez-Llano, M. & Waller, J.T. 2020. Selection on
phenotypic plasticity favors thermal canalization. Proceedings of the
National Academy of Sciences 117: 29767-29774.
Szczesnaskorupa, E., Browne, N., Mead, D. & Kemper, B. 1988. Positive
charges at the NH2 terminus convert the membrane-anchor signal peptide
of cytochrome P-450 to a secretory signal peptide. Proceedings of the
National Academy of Sciences of the United States of America 85:
738-742.
Takei, Y. & McCormick, S.D. 2012. Hormonal control of fish
euryhalinity. In: McCormick, S.D., Farrell, A.P. & Brauner, C.J., eds.
Fish Physiology. Academic Press, pp. 69-123.
Taugbøl, A., Arntsen, T., Østbye, K. & Vøllestad, L.A. 2014a. Small
changes in gene expression of targeted osmoregulatory genes when
exposing marine and freshwater threespine stickleback
(Gasterosteus aculeatus ) to abrupt salinity transfers. Plos One
9.
Taugbøl, A., Junge, C., Quinn, T.P., Herland, A. & Vøllestad, L.A.
2014b. Genetic and morphometric divergence in threespine stickleback in
the Chignik catchment, Alaska. Ecology and Evolution 4: 144-156.
Tian, X., Wang, X. & Li, Y. 2021. Myosin XI-B is involved in the
transport of vesicles and organelles in pollen tubes of Arabidopsis
thaliana. Plant J 108: 1145-1161.
Trapnell, C., Roberts, A., Goff, L., Pertea, G., Kim, D., Kelley, D.R.,
Pimentel, H., Salzberg, S.L., Rinn, J.L. & Pachter, L. 2012.
Differential gene and transcript expression analysis of RNA-seq
experiments with TopHat and Cufflinks. Nature Protocols 7: 562-578.
Varadharajan, S., Sandve, S.R., Gillard, G.B., Tørresen, O.K., Mulugeta,
T.D., Hvidsten, T.R., Lien, S., Vøllestad, L.A., Jentoft, S.,
Nederbragt, A.J. & Jakobsen, K.S. 2018. The grayling genome reveals
selection on gene expression regulation after whole-genome duplication.
Genome biology and evolution 10: 2785-2800.
Velotta, J.P., Wegrzyn, J.L., Ginzburg, S., Kang, L., Czesny, S.,
O’Neill, R.J., McCormick, S.D., Michalak, P. & Schultz, E.T. 2017.
Transcriptomic imprints of adaptation to fresh water: parallel evolution
of osmoregulatory gene expression in the Alewife. Molecular Ecology 26:
831-848.
Verri, T., Terova, G., Romano, A., Barca, A., Pisani, P., Storelli, C.
& Saroglia, M. 2012. The soLute carrier (SLC) family series in teleost
fish. Functional Genomics in Aquaculture. pp. 219-320.
Vijayan, M., Morgan, J., Sakamoto, T., Grau, E. & Iwama, G. 1996.
Food-deprivation affects seawater acclimation in tilapia: hormonal and
metabolic changes. Journal of Experimental Biology 199: 2467-2475.
Waddington, C.H. 1961. Genetic assimilation. In: Caspari, E.W. &
Thoday, J.M., eds. Advances in genetics. Academic Press, pp. 257-293.
Wang, G., Yang, E., Smith, K.J., Zeng, Y., Ji, G., Connon, R., Fangue,
N.A. & Cai, J.J. 2014. Gene expression responses of threespine
stickleback to salinity: implications for salt-sensitive hypertension.
Frontiers in genetics 5: 312-312.
Wang, Y., Sheng, H.-F., He, Y., Wu, J.-Y., Jiang, Y.-X., Tam, N.F.-Y. &
Zhou, H.-W. 2012. Comparison of the levels of bacterial diversity in
freshwater, intertidal wetland, and marine sediments by using millions
of illumina tags. Applied and Environmental Microbiology 78: 8264-8271.
Warnes, G.R., Bolker, B., Bonebakker, L., Gentleman, R., Huber, W.,
Liaw, A., Lumley, T., Maechler, M., Magnusson, A., Moeller, S.,
Schwartz, M. & Venables, B. 2020. gplots: Various R Programming Tools
for Plotting Data. R package version 3.1.1.
https://CRAN.R-project.org/package=gplots.
Whitehead, A., Roach, J.L., Zhang, S.J. & Galvez, F. 2012. Salinity-
and population-dependent genome regulatory response during osmotic
acclimation in the killifish (Fundulus heteroclitus ) gill.
Journal of Experimental Biology 215: 1293-1305.
Wolf, J.B.W., Bayer, T., Haubold, B., Schilhabel, M., Rosenstiel, P. &
Tautz, D. 2010. Nucleotide divergence vs. gene expression
differentiation: comparative transcriptome sequencing in natural
isolates from the carrion crow and its hybrid zone with the hooded crow.
Molecular Ecology 19: 162-175.
Wong, B.B.M. & Candolin, U. 2015. Behavioral responses to changing
environments. Behavioral Ecology 26: 665-673.
Yan, B., Wang, Z.-H. & Zhao, J.-L. 2013. Mechanism of osmoregulatory
adaptation in tilapia. Molecular Biology Reports 40: 925-931.