Volume 41 Issue 4
Jul.  2020
Turn off MathJax
Article Contents
Yan-Bo Sun, Yi Zhang, Kai Wang. Perspectives on studying molecular adaptations of amphibians in the genomic era. Zoological Research, 2020, 41(4): 351-364. doi: 10.24272/j.issn.2095-8137.2020.046
Citation: Yan-Bo Sun, Yi Zhang, Kai Wang. Perspectives on studying molecular adaptations of amphibians in the genomic era. Zoological Research, 2020, 41(4): 351-364. doi: 10.24272/j.issn.2095-8137.2020.046

Perspectives on studying molecular adaptations of amphibians in the genomic era

doi: 10.24272/j.issn.2095-8137.2020.046
Funds:  This study was supported by the National Natural Science Foundation of China (31671326, 31871275) and the High-level Talent Introduction Program of Yunnan University to Y.B.S
More Information
  • Corresponding author: E-mail: sunyanbo@ynu.edu.cn
  • Received Date: 2020-02-16
  • Accepted Date: 2020-04-23
  • Available Online: 2020-05-09
  • Publish Date: 2020-07-18
  • Understanding the genetic mechanisms underlying particular adaptations/phenotypes of organisms is one of the core issues of evolutionary biology. The use of genomic data has greatly advanced our understandings on this issue, as well as other aspects of evolutionary biology, including molecular adaptation, speciation, and even conservation of endangered species. Despite the well-recognized advantages, usages of genomic data are still limited to non-mammal vertebrate groups, partly due to the difficulties in assembling large or highly heterozygous genomes. Although this is particularly the case for amphibians, nonetheless, several comparative and population genomic analyses have shed lights into the speciation and adaptation processes of amphibians in a complex landscape, giving a promising hope for a wider application of genomics in the previously believed challenging groups of organisms. At the same time, these pioneer studies also allow us to realize numerous challenges in studying the molecular adaptations and/or phenotypic evolutionary mechanisms of amphibians. In this review, we first summarize the recent progresses in the study of adaptive evolution of amphibians based on genomic data, and then we give perspectives regarding how to effectively identify key pathways underlying the evolution of complex traits in the genomic era, as well as directions for future research.

  • loading
  • [1]
    Allendorf FW. 2017. Genetics and the conservation of natural populations: allozymes to genomes. Molecular Ecology, 26(2): 420−430. doi:  10.1111/mec.13948
    Allendorf FW, Hohenlohe PA, Luikart G. 2010. Genomics and the future of conservation genetics. Nature Reviews Genetics, 11(10): 697−709. doi:  10.1038/nrg2844
    Andrews KR, Good JM, Miller MR, Luikart G, Hohenlohe PA. 2016. Harnessing the power of RADseq for ecological and evolutionary genomics. Nature Reviews Genetics, 17(2): 81−92. doi:  10.1038/nrg.2015.28
    Artemov AV, Mugue NS, Rastorguev SM, Zhenilo S, Mazur AM, Tsygankova SV, Boulygina ES, Kaplun D, Nedoluzhko AV, Medvedeva YA, Prokhortchouk EB. 2017. Genome-wide DNA methylation profiling reveals epigenetic adaptation of stickleback to marine and freshwater conditions. Molecular Biology and Evolution, 34(9): 2203−2213. doi:  10.1093/molbev/msx156
    Beall CM, Cavalleri GL, Deng LB, Elston RC, Gao Y, Knight J, Li CH, Li JC, Liang Y, McCormack M, Montgomery HE, Pan H, Robbins PA, Shianna KV, Tam SC, Tsering N, Veeramah KR, Wang W, Wangdui P, Weale ME, Xu YM, Xu Z, Yang L, Zaman MJ, Zeng CQ, Zhang L, Zhang XL, Zhaxi PC, Zheng YT. 2010. Natural selection on EPAS1 (HIF2α) associated with low hemoglobin concentration in Tibetan highlanders. Proceedings of the National Academy of Sciences of the United States of America, 107(25): 11459−11464. doi:  10.1073/pnas.1002443107
    Beaumont MA, Balding DJ. 2004. Identifying adaptive genetic divergence among populations from genome scans. Molecular Ecology, 13(4): 969−980. doi:  10.1111/j.1365-294X.2004.02125.x
    Böcher TW. 1977. Convergence as an evolutionary process. Botanical Journal of the Linnean Society, 75(1): 1−19. doi:  10.1111/j.1095-8339.1977.tb01476.x
    Bossdorf O, Arcuri D, Richards CL, Pigliucci M. 2010. Experimental alteration of DNA methylation affects the phenotypic plasticity of ecologically relevant traits in Arabidopsis thaliana. Evolutionary Ecology, 24(3): 541−553. doi:  10.1007/s10682-010-9372-7
    Brandies P, Peel E, Hogg CJ, Belov K. 2019. The value of reference genomes in the conservation of threatened species. Genes, 10(11): 846. doi:  10.3390/genes10110846
    Che J, Wang K. 2016. AmphibiaChina: an online database of Chinese Amphibians. Zoological Research, 37(1): 57−59.
    Chen J, Swofford R, Johnson J, Cummings BB, Rogel N, Lindblad-Toh K, Haerty W, Di Palma F, Regev A. 2019. A quantitative framework for characterizing the evolutionary history of mammalian gene expression. Genome Research, 29(1): 53−63. doi:  10.1101/gr.237636.118
    Chikina M, Robinson JD, Clark NL. 2016. Hundreds of genes experienced convergent shifts in selective pressure in marine mammals. Molecular Biology and Evolution, 33(9): 2182−2192. doi:  10.1093/molbev/msw112
    Coop G, Witonsky D, Di Rienzo A, Pritchard JK. 2010. Using environmental correlations to identify loci underlying local adaptation. Genetics, 185(4): 1411−1423. doi:  10.1534/genetics.110.114819
    Dai TM, Lü ZC, Liu WX, Wan FH, Hong XY. 2017. The homology gene BtDnmt1 is essential for temperature tolerance in invasive Bemisia tabaci Mediterranean cryptic species. Scientific Reports, 7(1): 3040. doi:  10.1038/s41598-017-03373-w
    Daub JT, Hofer T, Cutivet E, Dupanloup I, Quintana-Murci L, Robinson-Rechavi M, Excoffier L. 2013. Evidence for polygenic adaptation to pathogens in the human genome. Molecular Biology and Evolution, 30(7): 1544−1558. doi:  10.1093/molbev/mst080
    Deamer D, Akeson M, Branton D. 2016. Three decades of nanopore sequencing. Nature Biotechnology, 34(5): 518−524. doi:  10.1038/nbt.3423
    Denton RD, Kudra RS, Malcom JW, Preez LD, Malone JH. 2018. The African Bullfrog (Pyxicephalus adspersus) genome unites the two ancestral ingredients for making vertebrate sex chromosomes. bioRxiv. doi:  10.1101/329847.
    Di Franco A, Poujol R, Baurain D, Philippe H. 2019. Evaluating the usefulness of alignment filtering methods to reduce the impact of errors on evolutionary inferences. BMC Evolutionary Biology, 19(1): 21. doi:  10.1186/s12862-019-1350-2
    Dobzhansky T, Gould SJ. 1982. Genetics and the Origin of Species. Columbia: Columbia University Press.
    Dubin MJ, Zhang P, Meng DZ, Remigereau MS, Osborne EJ, Casale FP, Drewe P, Kahles A, Jean G, Vilhjálmsson B, Jagoda J, Irez S, Voronin V, Song Q, Long Q, Rätsch G, Stegle O, Clark RM, Nordborg M. 2015. DNA methylation in Arabidopsis has a genetic basis and shows evidence of local adaptation. eLife, 4: e05255. doi:  10.7554/eLife.05255
    Edwards RJ, Tuipulotu DE, Amos TG, O'Meally D, Richardson MF, Russell TL, Vallinoto M, Carneiro M, Ferrand N, Wilkins MR, Sequeira F, Rollins LA, Holmes EC, Shine R, White PA. 2018. Draft genome assembly of the invasive cane toad, Rhinella marina. Gigascience, 7(9): giy095.
    Elewa A, Wang H, Talavera-López C, Joven A, Brito G, Kumar A, Hameed LS, Penrad-Mobayed M, Yao ZY, Zamani N, Abbas Y, Abdullayev I, Sandberg R, Grabherr M, Andersson B, Simon A. 2017. Reading and editing the Pleurodeles waltl genome reveals novel features of tetrapod regeneration. Nature Communications, 8(1): 2286. doi:  10.1038/s41467-017-01964-9
    Elliott TA, Gregory TR. 2015. What's in a genome? The C-value enigma and the evolution of eukaryotic genome content. Philosophical Transactions of the Royal Society B: Biological Sciences, 370(1678): 20140331. doi:  10.1098/rstb.2014.0331
    Esnault C, Lee M, Ham C, Levin HL. 2019. Transposable element insertions in fission yeast drive adaptation to environmental stress. Genome Research, 29(1): 85−95. doi:  10.1101/gr.239699.118
    Faulkner GJ, Kimura Y, Daub CO, Wani S, Plessy C, Irvine KM, Schroder K, Cloonan N, Steptoe AL, Lassmann T, Waki K, Hornig N, Arakawa T, Takahashi H, Kawai J, Forrest ARR, Suzuki H, Hayashizaki Y, Hume DA, Orlando V, Grimmond SM, Carninci P. 2009. The regulated retrotransposon transcriptome of mammalian cells. Nature Genetics, 41(5): 563−571. doi:  10.1038/ng.368
    Fedoroff NV. 2012. Presidential address. Transposable elements, epigenetics, and genome evolution. Science, 338(6108): 758−767.
    Felsenstein J. 1985. Phylogenies and the comparative method. The American Naturalist, 125(1): 1−15. doi:  10.1086/284325
    Ferea TL, Botstein D, Brown PO, Rosenzweig RF. 1999. Systematic changes in gene expression patterns following adaptive evolution in yeast. Proceedings of the National Academy of Sciences of the United States of America, 96(17): 9721−9726. doi:  10.1073/pnas.96.17.9721
    Field Y, Boyle EA, Telis N, Gao ZY, Gaulton KJ, Golan D, Yengo L, Rocheleau G, Froguel P, McCarthy MI, Pritchard JK. 2016. Detection of human adaptation during the past 2000 years. Science, 354(6313): 760−764. doi:  10.1126/science.aag0776
    Fletcher W, Yang ZH. 2010. The effect of insertions, deletions, and alignment errors on the branch-site test of positive selection. Molecular Biology and Evolution, 27(10): 2257−2267. doi:  10.1093/molbev/msq115
    Foll M, Gaggiotti OE, Daub JT, Vatsiou A, Excoffier L. 2014. Widespread signals of convergent adaptation to high altitude in Asia and america. The American Journal of Human Genetics, 95(4): 394−407. doi:  10.1016/j.ajhg.2014.09.002
    Foote AD, Liu Y, Thomas GWC, Vinař T, Alföldi J, Deng JX, Dugan S, Van Elk CE, Hunter ME, Joshi V, Khan Z, Kovar C, Lee SL, Lindblad-Toh K, Mancia A, Nielsen R, Qin X, Qu JX, Raney BJ, Vijay N, Wolf JBW, Hahn MW, Muzny DM, Worley KC, Gilbert MTP, Gibbs RA. 2015. Convergent evolution of the genomes of marine mammals. Nature Genetics, 47(3): 272−275. doi:  10.1038/ng.3198
    Fraser HB, Moses AM, Schadt EE. 2010. Evidence for widespread adaptive evolution of gene expression in budding yeast. Proceedings of the National Academy of Sciences of the United States of America, 107(7): 2977−2982. doi:  10.1073/pnas.0912245107
    Funk WC, Murphy MA, Hoke KL, Muths E, Amburgey SM, Lemmon EM, Lemmon AR. 2016. Elevational speciation in action? Restricted gene flow associated with adaptive divergence across an altitudinal gradient. Journal of Evolutionary Biology, 29(2): 241−252. doi:  10.1111/jeb.12760
    Funk WC, Zamudio KR, Crawford AJ. 2018. Advancing Understanding of Amphibian Evolution, Ecology, Behavior, and Conservation with Massively Parallel Sequencing. Cham: Springer.
    Ge RL, Cai QL, Shen YY, San A, Ma L, Zhang Y, Yi X, Chen Y, Yang LF, Huang Y, He RJ, Hui YY, Hao MR, Li Y, Wang B, Ou XH, Xu JH, Zhang YF, Wu K, Geng CY, Zhou WP, Zhou TC, Irwin DM, Yang YZ, Ying L, Bao HH, Kim J, Larkin DM, Ma J, Lewin HA, Xing JC, Platt II RN, Ray DA, Auvil L, Capitanu B, Zhang XF, Zhang GJ, Murphy RW, Wang J, Zhang YP, Wang J. 2013. Draft genome sequence of the Tibetan antelope. Nature Communications, 4: 1858. doi:  10.1038/ncomms2860
    Genome 10K Community of Scientists. 2009. Genome 10K: a proposal to obtain whole-genome sequence for 10000 vertebrate species. Journal of Heredity, 100(6): 659−674. doi:  10.1093/jhered/esp086
    Glenn TC. 2011. Field guide to next-generation DNA sequencers. Molecular Ecology Resources, 11(5): 759−769. doi:  10.1111/j.1755-0998.2011.03024.x
    Gnecchi-Ruscone GA, Abondio P, De Fanti S, Sarno S, Sherpa MG, Sherpa PT, Marinelli G, Natali L, Di Marcello M, Peluzzi D, Luiselli D, Pettener D, Sazzini M. 2018. Evidence of polygenic adaptation to high altitude from tibetan and sherpa genomes. Genome Biology and Evolution, 10(11): 2919−2930.
    Gouy A, Daub JT, Excoffier L. 2017. Detecting gene subnetworks under selection in biological pathways. Nucleic Acids Research, 45(16): e149. doi:  10.1093/nar/gkx626
    Guo BC, Lu D, Liao WB, Merila J. 2016. Genomewide scan for adaptive differentiation along altitudinal gradient in the Andrew's toad Bufo andrewsi. Molecular Ecology, 25(16): 3884−3900. doi:  10.1111/mec.13722
    Guo WF, Zhang SW, Zeng T, Li Y, Gao JX, Chen LN. 2019. A novel network control model for identifying personalized driver genes in cancer. PLoS Computational Biology, 15(11): e1007520. doi:  10.1371/journal.pcbi.1007520
    Hammond SA, Warren RL, Vandervalk BP, Kucuk E, Khan H, Gibb EA, Pandoh P, Kirk H, Zhao YJ, Jones M, Mungall AJ, Coope R, Pleasance S, Moore RA, Holt RA, Round JM, Ohora S, Walle BV, Veldhoen N, Helbing CC, Birol I. 2017. The North American bullfrog draft genome provides insight into hormonal regulation of long noncoding RNA. Nature Communications, 8(1): 1433. doi:  10.1038/s41467-017-01316-7
    Hancock AM, Witonsky DB, Ehler E, Alkorta-Aranburu G, Beall C, Gebremedhin A, Sukernik R, Utermann G, Pritchard J, Coop G, Di Rienzo A. 2010. Colloquium paper: human adaptations to diet, subsistence, and ecoregion are due to subtle shifts in allele frequency. Proceedings of the National Academy of Sciences of the United States of America, 107(Suppl 2): 8924−8930.
    Hansen TF. 1997. Stabilizing selection and the comparative analysis of adaptation. Evolution, 51(5): 1341−1351. doi:  10.1111/j.1558-5646.1997.tb01457.x
    Hao Y, Xiong Y, Cheng YL, Song G, Jia CX, Qu YH, Lei FM. 2019. Comparative transcriptomics of 3 high-altitude passerine birds and their low-altitude relatives. Proceedings of the National Academy of Sciences of the United States of America, 116(24): 11851−11856.
    Hawes NA, Fidler AE, Tremblay LA, Pochon X, Dunphy BJ, Smith KF. 2018. Understanding the role of DNA methylation in successful biological invasions: a review. Biological Invasions, 20(9): 2285−2300. doi:  10.1007/s10530-018-1703-6
    Hellsten U, Harland RM, Gilchrist MJ, Hendrix D, Jurka J, Kapitonov V, Ovcharenko I, Putnam NH, Shu SQ, Taher L, Blitz IL, Blumberg B, Dichmann DS, Dubchak I, Amaya E, Detter JC, Fletcher R, Gerhard DS, Goodstein D, Graves T, Grigoriev IV, Grimwood J, Kawashima T, Lindquist E, Lucas SM, Mead PE, Mitros T, Ogino H, Ohta Y, Poliakov AV, Pollet N, Robert J, Salamov A, Sater AK, Schmutz J, Terry A, Vize PD, Warren WC, Wells D, Wills A, Wilson RK, Zimmerman LB, Zorn AM, Grainger R, Grammer T, Khokha MK, Richardson PM, Rokhsar DS. 2010. The genome of the Western clawed frog Xenopus tropicalis. Science, 328(5978): 633−636. doi:  10.1126/science.1183670
    Herrera CM, Bazaga P. 2011. Untangling individual variation in natural populations: ecological, genetic and epigenetic correlates of long-term inequality in herbivory. Molecular Ecology, 20(8): 1675−1688. doi:  10.1111/j.1365-294X.2011.05026.x
    Hudson RR, Kreitman M, Aguade M. 1987. A test of neutral molecular evolution based on nucleotide data. Genetics, 116(1): 153−159.
    Idaghdour Y, Czika W, Shianna KV, Lee SH, Visscher PM, Martin HC, Miclaus K, Jadallah SJ, Goldstein DB, Wolfinger RD, Gibson G. 2009. Geographical genomics of human leukocyte gene expression variation in southern Morocco. Nature Genetics, 42(1): 62−67.
    King MC, Wilson AC. 1975. Evolution at two levels in humans and chimpanzees. Science, 188(4184): 107−116. doi:  10.1126/science.1090005
    Koepfli KP, Paten B, The Genome 10K Community of Scientists, O'brien SJ. 2015. The Genome 10K Project: a way forward. Annual Review of Animal Biosciences, 3: 57−111. doi:  10.1146/annurev-animal-090414-014900
    Kronholm I, Collins S. 2016. Epigenetic mutations can both help and hinder adaptive evolution. Molecular Ecology, 25(8): 1856−1868. doi:  10.1111/mec.13296
    Laird PW. 2010. Principles and challenges of genomewide DNA methylation analysis. Nature Reviews Genetics, 11(3): 191−203. doi:  10.1038/nrg2732
    Lamichhaney S, Berglund J, Almen MS, Maqbool K, Grabherr M, Martinez-Barrio A, Promerová M, Rubin CJ, Wang C, Zamani N, Grant BR, Grant PR, Webster MT, Andersson L. 2015. Evolution of Darwin's finches and their beaks revealed by genome sequencing. Nature, 518(7539): 371−375. doi:  10.1038/nature14181
    Lee KM, Coop G. 2019. Population genomics perspectives on convergent adaptation. Philosophical Transactions of the Royal Society B: Biological Sciences, 374(1777): 20180236. doi:  10.1098/rstb.2018.0236
    Li G, Wang JH, Rossiter SJ, Jones G, Cotton JA, Zhang SY. 2008. The hearing gene Prestin reunites echolocating bats. Proceedings of the National Academy of Sciences of the United States of America, 105(37): 13959−13964. doi:  10.1073/pnas.0802097105
    Li J, Yu HY, Wang WX, Fu C, Zhang W, Han FM, Wu H. 2019a. Genomic and transcriptomic insights into molecular basis of sexually dimorphic nuptial spines in Leptobrachium leishanense. Nature Communications, 10(1): 5551. doi:  10.1038/s41467-019-13531-5
    Li JT, Gao YD, Xie L, Deng C, Shi P, Guan ML, Huang S, Ren JL, Wu DD, Ding L, Huang ZY, Nie H, Humphreys DP, Hillis DM, Wang WZ, Zhang YP. 2018. Comparative genomic investigation of high-elevation adaptation in ectothermic snakes. Proceedings of the National Academy of Sciences of the United States of America, 115(33): 8406−8411. doi:  10.1073/pnas.1805348115
    Li Y, Liu Z, Shi P, Zhang JZ. 2010. The hearing gene Prestin unites echolocating bats and whales. Current Biology, 20(2): R55−R56. doi:  10.1016/j.cub.2009.11.042
    Li YX, Ren YD, Zhang DR, Jiang H, Wang ZK, Li XY, Rao DQ. 2019b. Chromosome-level assembly of the mustache toad genome using third-generation DNA sequencing and Hi-C analysis. Gigascience, 8(9): giz114. doi:  10.1093/gigascience/giz114
    Liang L, Shen YY, Pan XW, Zhou TC, Yang C, Irwin DM, Zhang YP. 2013. Adaptive evolution of the Hox gene family for development in bats and dolphins. PLoS One, 8(6): e65944. doi:  10.1371/journal.pone.0065944
    Liedtke HC, Gower DJ, Wilkinson M, Gomez-Mestre I. 2018. Macroevolutionary shift in the size of amphibian genomes and the role of life history and climate. Nature Ecology & Evolution, 2(11): 1792−1799.
    Löytynoja A, Goldman N. 2005. An algorithm for progressive multiple alignment of sequences with insertions. Proceedings of the National Academy of Sciences of the United States of America, 102(30): 10557−10562. doi:  10.1073/pnas.0409137102
    Marouli E, Graff M, Medina-Gomez C, et al. 2017. Rare and low-frequency coding variants alter human adult height. Nature, 542(7640): 186−190. doi:  10.1038/nature21039
    Melé M, Ferreira PG, Reverter F, DeLuca DS, Monlong J, Sammeth M, Young TR, Goldmann JM, Pervouchine DD, Sullivan TJ, Johnson R, Segrè AV, Djebali S, Niarchou A, The GTEx Consortium, Wright FA, Lappalainen T, Calvo M, Getz G, Dermitzakis ET, Ardlie KG, Guigó R. 2015. The human transcriptome across tissues and individuals. Science, 348(6235): 660−665. doi:  10.1126/science.aaa0355
    Miller WJ, McDonald JF, Nouaud D, Anxolabéhère D. 2000. Molecular domestication—more than a sporadic episode in evolution. In: McDonald JF. Transposable Elements and Genome Evolution. Dordrecht: Springer, 197–207.
    Mwangi J, Hao X, Lai R, Zhang ZY. 2019. Antimicrobial peptides: new hope in the war against multidrug resistance. Zoological Research, 40(6): 488−505. doi:  10.24272/j.issn.2095-8137.2019.062
    Nadeau NJ, Jiggins CD. 2010. A golden age for evolutionary genetics? Genomic studies of adaptation in natural populations. Trends in Genetics, 26(11): 484−492. doi:  10.1016/j.tig.2010.08.004
    Nowoshilow S, Schloissnig S, Fei JF, Dahl A, Pang AWC, Pippel M, Winkler S, Hastie AR, Young G, Roscito JG, Falcon F, Knapp D, Powell S, Cruz A, Cao H, Habermann B, Hiller M, Tanaka EM, Myers EW. 2018. The axolotl genome and the evolution of key tissue formation regulators. Nature, 554(7690): 50−55. doi:  10.1038/nature25458
    Orr HA. 1998. Testing natural selection vs. genetic drift in phenotypic evolution using quantitative trait locus data. Genetics, 149(4): 2099−2104.
    Ostrander EA, Wang GD, Larson G, Vonholdt BM, Davis BW, Jagannathan V, Hitte C, Wayne RK, Zhang YP, Dog10K Consortium. 2019. Dog10K: an international sequencing effort to advance studies of canine domestication, phenotypes and health. National Science Review, 6(4): 810−824. doi:  10.1093/nsr/nwz049
    Pickrell JK, Marioni JC, Pai AA, Degner JF, Engelhardt BE, Nkadori E, Veyrieras JB, Stephens M, Gilad Y, Pritchard JK. 2010. Understanding mechanisms underlying human gene expression variation with RNA sequencing. Nature, 464(7289): 768−772. doi:  10.1038/nature08872
    Plongthongkum N, Diep DH, Zhang K. 2014. Advances in the profiling of DNA modifications: cytosine methylation and beyond. Nature Reviews Genetics, 15(10): 647−661. doi:  10.1038/nrg3772
    Prohaska A, Racimo F, Schork AJ, Sikora M, Stern AJ, Ilardo M, Allentoft ME, Folkersen L, Buil A, Moreno-Mayar JV, Korneliussen T, Geschwind D, Ingason A, Werge T, Nielsen R, Willerslev E. 2019. Human disease variation in the light of population genomics. Cell, 177(1): 115−131. doi:  10.1016/j.cell.2019.01.052
    Rech GE, Bogaerts-Márquez M, Barrón MG, Merenciano M, Villanueva-Cañas JL, Horváth V, Fiston-Lavier AS, Luyten I, Venkataram S, Quesneville H, Petrov DA, González J. 2019. Stress response, behavior, and development are shaped by transposable element-induced mutations in Drosophila. PLoS Genetics, 15(2): e1007900. doi:  10.1371/journal.pgen.1007900
    Richards CL, Schrey AW, Pigliucci M. 2012. Invasion of diverse habitats by few Japanese knotweed genotypes is correlated with epigenetic differentiation. Ecology Letters, 15(9): 1016−1025. doi:  10.1111/j.1461-0248.2012.01824.x
    Richards EJ. 2006. Inherited epigenetic variation--revisiting soft inheritance. Nature Reviews Genetics, 7(5): 395−401. doi:  10.1038/nrg1834
    Rogers RL, Zhou L, Chu C, Márquez R, Corl A, Linderoth T, Freeborn L, MacManes MD, Xiong ZJ, Zheng J, Guo CX, Xun X, Kronforst MR, Summers K, Wu YF, Yang HM, Richards-Zawacki CL, Zhang GJ, Nielsen R. 2018. Genomic takeover by transposable elements in the strawberry poison frog. Molecular Biology and Evolution, 35(12): 2913−2927.
    Rohlf FJ. 2001. Comparative methods for the analysis of continuous variables: geometric interpretations. Evolution, 55(11): 2143−2160. doi:  10.1111/j.0014-3820.2001.tb00731.x
    Rohlfs RV, Nielsen R. 2015. Phylogenetic ANOVA: the expression variance and evolution model for quantitative trait evolution. Systematic Biology, 64(5): 695−708. doi:  10.1093/sysbio/syv042
    Rollins-Smith LA. 2009. The role of amphibian antimicrobial peptides in protection of amphibians from pathogens linked to global amphibian declines. Biochimica et Biophysica Acta (BBA) - Biomembranes, 1788(8): 1593−1599. doi:  10.1016/j.bbamem.2009.03.008
    Ruan J, Li H. 2020. Fast and accurate long-read assembly with wtdbg2. Nature Methods, 17(2): 155−158.
    Seidl F, Levis NA, Schell R, Pfennig DW, Pfennig KS, Ehrenreich IM. 2019. Genome of Spea multiplicata, a rapidly developing, phenotypically plastic, and desert-adapted spadefoot toad. G3: Genes, Genomes, Genetics, 9(12): 3909−3919.
    Seidl MF, Thomma BPHJ. 2017. Transposable elements direct the coevolution between plants and microbes. Trends in Genetics, 33(11): 842−851. doi:  10.1016/j.tig.2017.07.003
    Sela N, Mersch B, Gal-Mark N, Lev-Maor G, Hotz-Wagenblatt A, Ast G. 2007. Comparative analysis of transposed element insertion within human and mouse genomes reveals Alu's unique role in shaping the human transcriptome. Genome Biology, 8(6): R127. doi:  10.1186/gb-2007-8-6-r127
    Sela N, Mersch B, Hotz-Wagenblatt A, Ast G. 2010. Characteristics of transposable element exonization within human and mouse. PLoS One, 5(6): e10907. doi:  10.1371/journal.pone.0010907
    Session AM, Uno Y, Kwon T, et al. 2016. Genome evolution in the allotetraploid frog Xenopus laevis. Nature, 538(7625): 336−343. doi:  10.1038/nature19840
    Shaffer HB, Gidis M, McCartney-Melstad E, Neal KM, Oyamaguchi HM, Tellez M, Toffelmier EM. 2015. Conservation genetics and genomics of amphibians and reptiles. Annual Review of Animal Biosciences, 3: 113−138. doi:  10.1146/annurev-animal-022114-110920
    Shen JX, Feng AS, Xu ZM, Yu ZL, Arch VS, Yu XJ, Narins PM. 2008. Ultrasonic frogs show hyperacute phonotaxis to female courtship calls. Nature, 453(7197): 914−916. doi:  10.1038/nature06719
    Sinzelle L, Izsvák Z, Ivics Z. 2009. Molecular domestication of transposable elements: from detrimental parasites to useful host genes. Cellular and Molecular Life Sciences, 66(6): 1073−1093. doi:  10.1007/s00018-009-8376-3
    Smith JJ, Timoshevskaya N, Timoshevskiy VA, Keinath MC, Hardy D, Voss SR. 2019. A chromosome-scale assembly of the axolotl genome. Genome Research, 29(2): 317−324. doi:  10.1101/gr.241901.118
    Solak HM, Yanchukov A, Çolak F, Matur F, Sözen M, Ayanoğlu İC, Winternitz JC. 2020. Altitudinal Effects on Innate Immune Response of a Subterranean Rodent. Zoological Science, 37(1): 31−41. doi:  10.2108/zs190067
    Sorek R. 2007. The birth of new exons: mechanisms and evolutionary consequences. RNA, 13(10): 1603−1608. doi:  10.1261/rna.682507
    Stanke M, Steinkamp R, Waack S, Morgenstern B. 2004. AUGUSTUS: a web server for gene finding in eukaryotes. Nucleic Acids Research, 32(S2): W309-−W312.
    Storfer A, Eastman JM, Spear SF. 2009. Modern molecular methods for amphibian conservation. BioScience, 59(7): 559−571. doi:  10.1525/bio.2009.59.7.7
    Sun YB. 2017. FasParser: a package for manipulating sequence data. Zoological Research, 38(2): 110−112. doi:  10.24272/j.issn.2095-8137.2017.017
    Sun YB. 2018. FasParser2: a graphical platform for batch manipulation of tremendous amount of sequence data. Bioinformatics, 34(14): 2493−2495. doi:  10.1093/bioinformatics/bty126
    Sun YB, Fu TT, Jin JQ, Murphy RW, Hillis DM, Zhang YP, Che J. 2018. Species groups distributed across elevational gradients reveal convergent and continuous genetic adaptation to high elevations. Proceedings of the National Academy of Sciences of the United States of America, 115(45): E10634−E10641. doi:  10.1073/pnas.1813593115
    Sun YB, Xiong ZJ, Xiang XY, Liu SP, Zhou WW, Tu XL, Zhong L, Wang L, Wu DD, Zhang BL, Zhu CL, Yang MM, Chen HM, Li F, Zhou L, Feng SH, Huang C, Zhang GJ, Irwin D, Hillis DM, Murphy RW, Yang HM, Che J, Wang J, Zhang YP. 2015. Whole-genome sequence of the Tibetan frog Nanorana parkeri and the comparative evolution of tetrapod genomes. Proceedings of the National Academy of Sciences of the United States of America, 112(11): E1257−E1262. doi:  10.1073/pnas.1501764112
    Supple MA, Shapiro B. 2018. Conservation of biodiversity in the genomics era. Genome Biology, 19(1): 131. doi:  10.1186/s13059-018-1520-3
    The ENCODE Project Consortium. 2012. An integrated encyclopedia of DNA elements in the human genome. Nature, 489(7414): 57−74. doi:  10.1038/nature11247
    Thomas GWC, Hahn MW. 2015. Determining the null model for detecting adaptive convergence from genomic data: a case study using echolocating mammals. Molecular Biology and Evolution, 32(5): 1232−1236. doi:  10.1093/molbev/msv013
    Tian H, Hammer RE, Matsumoto AM, Russell DW, McKnight SL. 1998. The hypoxia-responsive transcription factor EPAS1 is essential for catecholamine homeostasis and protection against heart failure during embryonic development. Genes & Development, 12(21): 3320−3324.
    Vitti JJ, Grossman SR, Sabeti PC. 2013. Detecting natural selection in genomic data. Annual Review of Genetics, 47: 97−120. doi:  10.1146/annurev-genet-111212-133526
    Wang B, Chen L, Wang W. 2019. Genomic insights into ruminant evolution: from past to future prospects. Zoological Research, 40(6): 476−487. doi:  10.24272/j.issn.2095-8137.2019.061
    Wang GD, Zhang BL, Zhou WW, Li YX, Jin JQ, Shao Y, Yang HC, Liu YH, Yan F, Chen HM, Jin L, Gao F, Zhang YG, Li HP, Mao BY, Murphy RW, Wake DB, Zhang YP, Che J. 2018. Selection and environmental adaptation along a path to speciation in the Tibetan frog Nanorana parkeri. Proceedings of the National Academy of Sciences of the United States of America, 115(22): E5056−E5065. doi:  10.1073/pnas.1716257115
    Wang Z, Gerstein M, Snyder M. 2009. RNA-Seq: a revolutionary tool for transcriptomics. Nature Reviews Genetics, 10(1): 57−63. doi:  10.1038/nrg2484
    Ward RD, Skibinski DOF, Woodwark M. 1992. Protein heterozygosity, protein structure, and taxonomic differentiation. In: Hecht MK, Wallace B, Macintyre RJ. Evolutionary Biology. Boston: Springer, 73–159.
    Whelan S, Irisarri I, Burki F. 2018. PREQUAL: detecting non-homologous characters in sets of unaligned homologous sequences. Bioinformatics, 34(22): 3929−3930.
    Wood AR, Esko T, Yang J, et al. 2014. Defining the role of common variation in the genomic and biological architecture of adult human height. Nature Genetics, 46(11): 1173−1186. doi:  10.1038/ng.3097
    Yang CH, Fu TT, Lan XQ, Zhang Y, Nneji LM, Murphy RW, Sun YB, Che J. 2019. Comparative skin histology of frogs reveals high-elevation adaptation of the tibetan Nanorana parkeri. Asian Herpetological Research, 10(2): 79−85.
    Yang JR, Maclean CJ, Park C, Zhao HB, Zhang JZ. 2017. Intra and interspecific variations of gene expression levels in yeast are largely neutral: (Nei lecture, SMBE 2016, gold coast). Molecular Biology and Evolution, 34(9): 2125−2139. doi:  10.1093/molbev/msx171
    Yang WZ, Qi Y, Bi K, Fu JZ. 2012. Toward understanding the genetic basis of adaptation to high-elevation life in poikilothermic species: a comparative transcriptomic analysis of two ranid frogs, Rana chensinensis and R. kukunoris. BMC Genomics, 13: 588. doi:  10.1186/1471-2164-13-588
    Yang XW, Wang Y, Zhang Y, Lee WH, Zhang Y. 2016. Rich diversity and potency of skin antioxidant peptides revealed a novel molecular basis for high-altitude adaptation of amphibians. Scientific Reports, 6: 19866. doi:  10.1038/srep19866
    Yu XT, Zhang JS, Sun SY, Zhou X, Zeng T, Chen LN. 2017. Individual-specific edge-network analysis for disease prediction. Nucleic Acids Research, 45(20): e170. doi:  10.1093/nar/gkx787
    Zhang GJ, Li C, Li QY, et al. 2014. Comparative genomics reveals insights into avian genome evolution and adaptation. Science, 346(6215): 1311−1320. doi:  10.1126/science.1251385
    Zhang GJ. 2015. Genomics: bird sequencing project takes off. Nature, 522(7554): 34.
    Zhang JZ, Nielsen R, Yang ZH. 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
    Zhang YH, Cheng TC, Huang GR, Lu QY, Surleac MD, Mandell JD, Pontarotti P, Petrescu AJ, Xu AL, Xiong Y, Schatz DG. 2019. Transposon molecular domestication and the evolution of the RAG recombinase. Nature, 569(7754): 79−84. doi:  10.1038/s41586-019-1093-7
  • Relative Articles

    [1] Patrick K. Malonza, David M. Mulwa, Joash O. Nyamache, Georgina Jones. Biogeography of the Shimba Hills ecosystem herpetofauna in Kenya. Zoological Research, 2018, 39(2): 97-104.  doi: 10.24272/j.issn.2095-8137.2017.048
    [2] Jing CHE, Kai WANG. AmphibiaChina: an online database of Chinese Amphibians. Zoological Research, 2016, 37(1): 57-59.  doi: 10.13918/j.issn.2095-8137.2016.1.57
    [3] Ming-Shan WANG, Adeniyi C. ADEOLA, Yan LI, Ya-Ping ZHANG, Dong-Dong WU. Accelerated evolution of constraint elements for hematophagic adaptation in mosquitoes. Zoological Research, 2015, 36(6): 320-327.  doi: 10.13918/j.issn.ZoolRes.2015.6.320
    [4] Xiao-Ai CHANG, Yun XIA, Xiao-Mao ZENG. Application of ND-FISH in amphibians. Zoological Research, 2013, 34(6): 610-616.  doi: 10.11813/j.issn.0254-5853.2013.6.0610
    [5] CHEN Xing, SHEN Yong-Yi, ZHANG Ya-Ping. Review of mtDNA in molecular evolution studies. Zoological Research, 2012, 33(6): 566-573.  doi: 10.3724/SP.J.1141.2012.06566
    [6] WANG Xi, WANG Yan-Ping, DING Ping. Nested species subsets of amphibians and reptiles in Thousand Island Lake. Zoological Research, 2012, 33(5): 439-446.  doi: 10.3724/SP.J.1141.2012.05439
    [7] XIE Yu-wei, XUE Xiao-ping, YIN Huan-cai, TANG Rui-hua, SU Jing, SONG Kai, HUYAN Ting, WANG Hua, YANG Hui. Homology Modeling and Molecular Evolution Analysis of Myostatin. Zoological Research, 2008, 29(5): 485-492.  doi: 10.3724/SP.J.1141.200805485
    [8] GAO Jia-li, LUO Yu-ping*, LI Si-guang. Molecular Evolution of miR-34 Gene Family. Zoological Research, 2007, 28(3): 271-278.
    [9] ZHANG Yun*. Amphibian Skin Secretions and Bio-adaptive Significance —Implications from Bombina maxima Skin Secretion Proteome. Zoological Research, 2006, 27(1): 101-112.
    [10] YU Xiao-dong, LUO Tian-hong, WU Yu-ming, ZHOU Hong-zhang. A Large-Scale Pattern in Species Diversity of Amphibians in the Yangtze River Basin. Zoological Research, 2005, 26(6): 565-579.
    [11] DONG Peng, WANG Jin-jun. Molecular Detection of Wolbachia wsp Gene in Liposcelis tricolor (Psocoptera:Liposcelididae). Zoological Research, 2004, 25(5): 456-459.
    [12] ZHOU Kai-Ya. Molecular Phylogenetics of Amphibians and Reptiles. Zoological Research, 2001, 22(5): 397-405.
    [13] LI Shu-shen. Transposable Element and The Speciation. Zoological Research, 1999, 20(5): 385-390.
    [14] ZHENG Xiang-zhong, ZHANG Ya-ping, ZHU Ding-liang, GENG Zhen-cheng. The Molecular Biology of The Biological Clock Gene,Period The Molecular Biology of The Biological Clock Gene,Period. Zoological Research, 1998, 19(6): 473-481.
    [15] HUANG Jing-fei, LIU Ci-quan. An Exploration of Histone Molecular Evolution From The Static Accessibility of Amino Acid Residues. Zoological Research, 1997, 18(4): 429-435.
    [16] HUANG Jing-fei, LIU Ci-quan. The Relationship Between Cytochrome Hydrophobicity and Molecular Evolution. Zoological Research, 1996, 17(2): 179-185.
    [17] YE Chang-yuan, FEI Liang, CHEN Su-wen. Polymorphism and Geographic Distribution of Skin Texture of Six Species Amphibians in Hengduan Mountains. Zoological Research, 1994, 15(1): 33-45.
    [18] LI Yong-tong, WU Zhi-kang. Ldh Isozyme Comparative Studies of Various Tissues in Four Species of Amphibians. Zoological Research, 1991, 12(2): 193-198.
    [19] WEI Gang, CHEN Fu-guan, LI De-jun. Preliminary Studies on Geographical Distribution and Faunal Regions of Amphibians of Guizhou Province. Zoological Research, 1989, 10(3): 241-249.
    [20] HUANG Jing-fei. The Research of 5S rRNA Molecular Evolution. Zoological Research, 1988, 9(4): 357-372.
  • 加载中


    通讯作者: 陈斌, bchen63@163.com
    • 1. 

      沈阳化工大学材料科学与工程学院 沈阳 110142

    1. 本站搜索
    2. 百度学术搜索
    3. 万方数据库搜索
    4. CNKI搜索

    Figures(1)  / Tables(1)

    Article Metrics

    Article views (1967) PDF downloads(153) Cited by()
    Proportional views


    DownLoad:  Full-Size Img  PowerPoint