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. 2023 Jan 13;66(3):453–495. doi: 10.1007/s11427-022-2233-x

Molecular mechanisms of adaptive evolution in wild animals and plants

Yibo Hu 1,✉,#, Xiaoping Wang 3,#, Yongchao Xu 4,#, Hui Yang 5,#, Zeyu Tong 6,#, Ran Tian 7,#, Shaohua Xu 8,#, Li Yu 3,✉, Yalong Guo 4,✉, Peng Shi 5,✉, Shuangquan Huang 6,✉, Guang Yang 2,7,✉, Suhua Shi 8,✉, Fuwen Wei 1,2,✉
PMCID: PMC9843154  PMID: 36648611

Abstract

Wild animals and plants have developed a variety of adaptive traits driven by adaptive evolution, an important strategy for species survival and persistence. Uncovering the molecular mechanisms of adaptive evolution is the key to understanding species diversification, phenotypic convergence, and inter-species interaction. As the genome sequences of more and more non-model organisms are becoming available, the focus of studies on molecular mechanisms of adaptive evolution has shifted from the candidate gene method to genetic mapping based on genome-wide scanning. In this study, we reviewed the latest research advances in wild animals and plants, focusing on adaptive traits, convergent evolution, and coevolution. Firstly, we focused on the adaptive evolution of morphological, behavioral, and physiological traits. Secondly, we reviewed the phenotypic convergences of life history traits and responding to environmental pressures, and the underlying molecular convergence mechanisms. Thirdly, we summarized the advances of coevolution, including the four main types: mutualism, parasitism, predation and competition. Overall, these latest advances greatly increase our understanding of the underlying molecular mechanisms for diverse adaptive traits and species interaction, demonstrating that the development of evolutionary biology has been greatly accelerated by multi-omics technologies. Finally, we highlighted the emerging trends and future prospects around the above three aspects of adaptive evolution.

Keywords: adaptive evolution, adaptive trait, coevolution, comparative genomics, convergent evolution, genetic convergence, molecular mechanism, mutualism, parasitism, phenotype convergence

Acknowledgements

This work was supported by the National Natural Science Foundation of China (31821001), and the Strategic Priority Research Program of Chinese Academy of Sciences (XDB31000000). We thank Simin Chai for help with manuscript preparation.

Footnotes

Compliance and ethics

The author(s) declare that they have no conflict of interest.

Contributed equally to this work

Contributor Information

Yibo Hu, Email: ybhu@ioz.ac.cn.

Li Yu, Email: yuli@ynu.edu.cn.

Yalong Guo, Email: yalong.guo@ibcas.ac.cn.

Peng Shi, Email: ship@mail.kiz.ac.cn.

Shuangquan Huang, Email: hsq@ccnu.edu.cn.

Guang Yang, Email: gyang@njnu.edu.cn.

Suhua Shi, Email: lssssh@mail.sysu.edu.cn.

Fuwen Wei, Email: weifw@ioz.ac.cn.

References

  1. Abzhanov A. Darwin’s Galápagos finches in modern biology. Phil Trans R Soc B. 2010;365:1001–1007. doi: 10.1098/rstb.2009.0321. [DOI] [PMC free article] [PubMed] [Google Scholar]
  2. Abzhanov A, Kuo WP, Hartmann C, Grant BR, Grant PR, Tabin CJ. The calmodulin pathway and evolution of elongated beak morphology in Darwin’s finches. Nature. 2006;442:563–567. doi: 10.1038/nature04843. [DOI] [PubMed] [Google Scholar]
  3. Abzhanov A, Protas M, Grant BR, Grant PR, Tabin CJ. Bmp4 and morphological variation of beaks in Darwin’s finches. Science. 2004;305:1462–1465. doi: 10.1126/science.1098095. [DOI] [PubMed] [Google Scholar]
  4. Adamec L. Mineral nutrition of carnivorous plants: a review. Bot Rev. 1997;63:273–299. doi: 10.1007/BF02857953. [DOI] [Google Scholar]
  5. Adli M. The CRISPR tool kit for genome editing and beyond. Nat Commun. 2018;9:1911. doi: 10.1038/s41467-018-04252-2. [DOI] [PMC free article] [PubMed] [Google Scholar]
  6. Agrawal AA, Petschenka G, Bingham RA, Weber MG, Rasmann S. Toxic cardenolides: chemical ecology and coevolution of specialized plant-herbivore interactions. New Phytol. 2012;194:28–45. doi: 10.1111/j.1469-8137.2011.04049.x. [DOI] [PubMed] [Google Scholar]
  7. Aguirre-Liguori JA, Ramírez-Barahona S, Gaut BS. The evolutionary genomics of species’ responses to climate change. Nat Ecol Evol. 2021;5:1350–1360. doi: 10.1038/s41559-021-01526-9. [DOI] [PubMed] [Google Scholar]
  8. Aguirre-Liguori JA, Ramírez-Barahona S, Tiffin P, Eguiarte LE. Climate change is predicted to disrupt patterns of local adaptation in wild and cultivated maize. Proc R Soc B. 2019;286:20190486. doi: 10.1098/rspb.2019.0486. [DOI] [PMC free article] [PubMed] [Google Scholar]
  9. Aguirre-Liguori JA, Tenaillon MI, Vázquez-Lobo A, Gaut BS, Jaramillo-Correa JP, Montes-Hernandez S, Souza V, Eguiarte LE. Connecting genomic patterns of local adaptation and niche suitability in teosintes. Mol Ecol. 2017;26:4226–4240. doi: 10.1111/mec.14203. [DOI] [PubMed] [Google Scholar]
  10. Ai B, Wang ZS, Ge S. Genome size is not correlated with effective population size in the Oryza species. Evolution. 2012;66:3302–3310. doi: 10.1111/j.1558-5646.2012.01674.x. [DOI] [PubMed] [Google Scholar]
  11. Almén MS, Lamichhaney S, Berglund J, Grant BR, Grant PR, Webster MT, Andersson L. Adaptive radiation of Darwin’s finches revisited using whole genome sequencing. BioEssays. 2016;38:14–20. doi: 10.1002/bies.201500079. [DOI] [PubMed] [Google Scholar]
  12. Alonge M, Wang X, Benoit M, Soyk S, Pereira L, Zhang L, Suresh H, Ramakrishnan S, Maumus F, Ciren D, et al. Major impacts of widespread structural variation on gene expression and crop improvement in tomato. Cell. 2020;182:145–161.e23. doi: 10.1016/j.cell.2020.05.021. [DOI] [PMC free article] [PubMed] [Google Scholar]
  13. Alonso-Blanco C, Aarts MGM, Bentsink L, Keurentjes JJB, Reymond M, Vreugdenhil D, Koornneef M. What has natural variation taught us about plant development, physiology, and adaptation? Plant Cell. 2009;21:1877–1896. doi: 10.1105/tpc.109.068114. [DOI] [PMC free article] [PubMed] [Google Scholar]
  14. Amrad A, Moser M, Mandel T, de Vries M, Schuurink RC, Freitas L, Kuhlemeier C. Gain and loss of floral scent production through changes in structural genes during pollinator-mediated speciation. Curr Biol. 2016;26:3303–3312. doi: 10.1016/j.cub.2016.10.023. [DOI] [PubMed] [Google Scholar]
  15. Andrews MT. Molecular interactions underpinning the phenotype of hibernation in mammals. J Exp Biol. 2019;222:jeb160606. doi: 10.1242/jeb.160606. [DOI] [PubMed] [Google Scholar]
  16. Antón M, Salesa MJ, Pastor JF, Peigné S, Morales J. Implications of the functional anatomy of the hand and forearm of Ailurus fulgens (Carnivora, Ailuridae) for the evolution of the “false-thumb” in pandas. J Anatomy. 2006;209:757–764. doi: 10.1111/j.1469-7580.2006.00649.x. [DOI] [PMC free article] [PubMed] [Google Scholar]
  17. Arabidopsis Genome Initiative Analysis of the genome sequence of the flowering plant Arabidopsis thaliana. Nature. 2000;408:796–815. doi: 10.1038/35048692. [DOI] [PubMed] [Google Scholar]
  18. Armbruster WS. Exaptations link evolution of plant-herbivore and plant-pollinator interactions: a phylogenetic inquiry. Ecology. 1997;78:1661. [Google Scholar]
  19. Ashfield T, Ong LE, Nobuta K, Schneider CM, Innes RW. Convergent evolution of disease resistance gene specificity in two flowering plant families. Plant Cell. 2004;16:309–318. doi: 10.1105/tpc.016725. [DOI] [PMC free article] [PubMed] [Google Scholar]
  20. Avila-Magaña V, Kamel B, DeSalvo M, Gómez-Campo K, Enríquez S, Kitano H, Rohlfs RV, Iglesias-Prieto R, Medina M. Elucidating gene expression adaptation of phylogenetically divergent coral holobionts under heat stress. Nat Commun. 2021;12:5731. doi: 10.1038/s41467-021-25950-4. [DOI] [PMC free article] [PubMed] [Google Scholar]
  21. Baduel P, Leduque B, Ignace A, Gy I, Gil J, Jr, Loudet O, Colot V, Quadrana L. Genetic and environmental modulation of transposition shapes the evolutionary potential of Arabidopsis thaliana. Genome Biol. 2021;22:138. doi: 10.1186/s13059-021-02348-5. [DOI] [PMC free article] [PubMed] [Google Scholar]
  22. Barrett RDH, Laurent S, Mallarino R, Pfeifer SP, Xu CCY, Foll M, Wakamatsu K, Duke-Cohan JS, Jensen JD, Hoekstra HE. Linking a mutation to survival in wild mice. Science. 2019;363:499–504. doi: 10.1126/science.aav3824. [DOI] [PubMed] [Google Scholar]
  23. Batstone RT, O’Brien AM, Harrison TL, Frederickson ME. Experimental evolution makes microbes more cooperative with their local host genotype. Science. 2020;370:476–478. doi: 10.1126/science.abb7222. [DOI] [PubMed] [Google Scholar]
  24. Bay RA, Harrigan RJ, Underwood VL, Gibbs HL, Smith TB, Ruegg K. Genomic signals of selection predict climate-driven population declines in a migratory bird. Science. 2018;359:83–86. doi: 10.1126/science.aan4380. [DOI] [PubMed] [Google Scholar]
  25. Beall CM. Tibetan and Andean patterns of adaptation to high-altitude hypoxia. Hum Biol. 2000;72:201–228. [PubMed] [Google Scholar]
  26. Beall CM. Adaptation to high altitude: phenotypes and genotypes. Annu Rev Anthropol. 2014;43:251–272. doi: 10.1146/annurev-anthro-102313-030000. [DOI] [Google Scholar]
  27. Beall CM, Cavalleri GL, Deng L, Elston RC, Gao Y, Knight J, Li C, Li JC, Liang Y, McCormack M, et al. Natural selection on EPAS1 (HIF2α) associated with low hemoglobin concentration in Tibetan highlanders. Proc Natl Acad Sci USA. 2010;107:11459–11464. doi: 10.1073/pnas.1002443107. [DOI] [PMC free article] [PubMed] [Google Scholar]
  28. Bennett TH, Flowers TJ, Bromham L. Repeated evolution of salt-tolerance in grasses. Biol Lett. 2013;9:20130029. doi: 10.1098/rsbl.2013.0029. [DOI] [PMC free article] [PubMed] [Google Scholar]
  29. Bento G, Routtu J, Fields PD, Bourgeois Y, Pasquier LD, Ebert D. The genetic basis of resistance and matching-allele interactions of a host-parasite system: The Daphnia magna-Pasteuria ramose model. PLoS Genet. 2017;13:e1006596. doi: 10.1371/journal.pgen.1006596. [DOI] [PMC free article] [PubMed] [Google Scholar]
  30. Bentsink L, Hanson J, Hanhart CJ, Blankestijn-de Vries H, Coltrane C, Keizer P, El-Lithy M, Alonso-Blanco C, de Andrés MT, Reymond M, et al. Natural variation for seed dormancy in Arabidopsis is regulated by additive genetic and molecular pathways. Proc Natl Acad Sci USA. 2010;107:4264–4269. doi: 10.1073/pnas.1000410107. [DOI] [PMC free article] [PubMed] [Google Scholar]
  31. Bentsink L, Jowett J, Hanhart CJ, Koornneef M. Cloning of DOG1, a quantitative trait locus controlling seed dormancy in Arabidopsis. Proc Natl Acad Sci USA. 2006;103:17042–17047. doi: 10.1073/pnas.0607877103. [DOI] [PMC free article] [PubMed] [Google Scholar]
  32. Berens AJ, Hunt JH, Toth AL. Comparative transcriptomics of convergent evolution: different genes but conserved pathways underlie caste phenotypes across lineages of eusocial insects. Mol Biol Evol. 2015;32:690–703. doi: 10.1093/molbev/msu330. [DOI] [PubMed] [Google Scholar]
  33. Bernsdorff C, Wolf A, Winter R, Gratton E. Effect of hydrostatic pressure on water penetration and rotational dynamics in phospholipid-cholesterol bilayers. Biophys J. 1997;72:1264–1277. doi: 10.1016/S0006-3495(97)78773-3. [DOI] [PMC free article] [PubMed] [Google Scholar]
  34. Berta, A., Sumich, J.L., and Kovacs, K.M. (2005). Marine Mammals: Evolutionary Biology. Elsevier.
  35. Besnard G, Muasya AM, Russier F, Roalson EH, Salamin N, Christin PA. Phylogenomics of C4 photosynthesis in sedges (Cyperaceae): multiple appearances and genetic convergence. Mol Biol Evol. 2009;26:1909–1919. doi: 10.1093/molbev/msp103. [DOI] [PubMed] [Google Scholar]
  36. Bewley JD. Seed germination and dormancy. Plant Cell. 1997;9:1055–1066. doi: 10.1105/tpc.9.7.1055. [DOI] [PMC free article] [PubMed] [Google Scholar]
  37. Birchler JA, Veitia RA. The gene balance hypothesis: from classical genetics to modern genomics. Plant Cell. 2007;19:395–402. doi: 10.1105/tpc.106.049338. [DOI] [PMC free article] [PubMed] [Google Scholar]
  38. Bourgeois Y, Roulin AC, Müller K, Ebert D. Parasitism drives host genome evolution: insights from the Pasteuria ramosa-Daphnia magna system. Evolution. 2017;71:1106–1113. doi: 10.1111/evo.13209. [DOI] [PubMed] [Google Scholar]
  39. Bradley TJ. Animal Osmoregulation. Oxford: Oxford University Press; 2009. [Google Scholar]
  40. Bubac CM, Miller JM, Coltman DW. The genetic basis of animal behavioural diversity in natural populations. Mol Ecol. 2020;29:1957–1971. doi: 10.1111/mec.15461. [DOI] [PubMed] [Google Scholar]
  41. Burns R, Mandáková T, Gunis J, Soto-Jiménez LM, Liu C, Lysak MA, Novikova PY, Nordborg M. Gradual evolution of allopolyploidy in Arabidopsis suecica. Nat Ecol Evol. 2021;5:1367–1381. doi: 10.1038/s41559-021-01525-w. [DOI] [PMC free article] [PubMed] [Google Scholar]
  42. Busoms S, Paajanen P, Marburger S, Bray S, Huang XY, Poschenrieder C, Yant L, Salt DE. Fluctuating selection on migrant adaptive sodium transporter alleles in coastal Arabidopsis thaliana. Proc Natl Acad Sci USA. 2018;115:E12443–E12452. doi: 10.1073/pnas.1816964115. [DOI] [PMC free article] [PubMed] [Google Scholar]
  43. Cai L, Arnold BJ, Xi Z, Khost DE, Patel N, Hartmann CB, Manickam S, Sasirat S, Nikolov LA, Mathews S, et al. Deeply altered genome architecture in the endoparasitic flowering plant Sapria himalayana Griff. (Rafflesiaceae) Curr Biol. 2021;31:1002–1011.e9. doi: 10.1016/j.cub.2020.12.045. [DOI] [PubMed] [Google Scholar]
  44. Cai Z, Zhou L, Ren NN, Xu X, Liu R, Huang L, Zheng XM, Meng QL, Du YS, Wang MX, et al. Parallel speciation of wild rice associated with habitat shifts. Mol Biol Evol. 2019;36:875–889. doi: 10.1093/molbev/msz029. [DOI] [PMC free article] [PubMed] [Google Scholar]
  45. Cao J, Schneeberger K, Ossowski S, Günther T, Bender S, Fitz J, Koenig D, Lanz C, Stegle O, Lippert C, et al. Wholegenome sequencing of multiple Arabidopsis thaliana populations. Nat Genet. 2011;43:956–963. doi: 10.1038/ng.911. [DOI] [PubMed] [Google Scholar]
  46. Carley LN, Mojica JP, Wang B, Chen CY, Lin YP, Prasad KVS K, Chan E, Hsu CW, Keith R, Nuñez CL, et al. Ecological factors influence balancing selection on leaf chemical profiles of a wildflower. Nat Ecol Evol. 2021;5:1135–1144. doi: 10.1038/s41559-021-01486-0. [DOI] [PMC free article] [PubMed] [Google Scholar]
  47. Caro T, Mallarino R. Coloration in mammals. Trends Ecol Evol. 2020;35:357–366. doi: 10.1016/j.tree.2019.12.008. [DOI] [PMC free article] [PubMed] [Google Scholar]
  48. Carter ME, Helm M, Chapman AVE, Wan E, Restrepo Sierra AM, Innes RW, Bogdanove AJ, Wise RP. Convergent evolution of effector protease recognition by Arabidopsis and barley. Mol Plant Microbe Interact. 2018;32:550–565. doi: 10.1094/MPMI-07-18-0202-FI. [DOI] [PubMed] [Google Scholar]
  49. Castoe TA, de Koning APJ, Kim HM, Gu W, Noonan BP, Naylor G, Jiang ZJ, Parkinson CL, Pollock DD. Evidence for an ancient adaptive episode of convergent molecular evolution. Proc Natl Acad Sci USA. 2009;106:8986–8991. doi: 10.1073/pnas.0900233106. [DOI] [PMC free article] [PubMed] [Google Scholar]
  50. Chaves JA, Cooper EA, Hendry AP, Podos J, De León LF, Raeymaekers JAM, MacMillan WO, Uy JAC. Genomic variation at the tips of the adaptive radiation of Darwin’s finches. Mol Ecol. 2016;25:5282–5295. doi: 10.1111/mec.13743. [DOI] [PubMed] [Google Scholar]
  51. Cheeseman JM. The evolution of halophytes, glycophytes and crops, and its implications for food security under saline conditions. New Phytol. 2015;206:557–570. doi: 10.1111/nph.13217. [DOI] [PubMed] [Google Scholar]
  52. Chen J, Huang Q, Gao D, Wang J, Lang Y, Liu T, Li B, Bai Z, Luis Goicoechea J, Liang C, et al. Whole-genome sequencing of Oryza brachyantha reveals mechanisms underlying Oryza genome evolution. Nat Commun. 2013;4:1595. doi: 10.1038/ncomms2596. [DOI] [PMC free article] [PubMed] [Google Scholar]
  53. Chen J, Huang Y, Brachi B, Yun Q, Zhang W, Lu W, Li H, Li W, Sun X, Wang G, et al. Genome-wide analysis of Cushion willow provides insights into alpine plant divergence in a biodiversity hotspot. Nat Commun. 2019;10:5230. doi: 10.1038/s41467-019-13128-y. [DOI] [PMC free article] [PubMed] [Google Scholar]
  54. Chen M, Penfield S. Feedback regulation of COOLAIR expression controls seed dormancy and flowering time. Science. 2018;360:1014–1017. doi: 10.1126/science.aar7361. [DOI] [PubMed] [Google Scholar]
  55. Chen Q, Jiang T, Liu YX, Liu H, Zhao T, Liu Z, Gan X, Hallab A, Wang X, He J, et al. Recently duplicated sesterterpene (C25) gene clusters in Arabidopsis thaliana modulate root microbiota. Sci China Life Sci. 2019;62:947–958. doi: 10.1007/s11427-019-9521-2. [DOI] [PubMed] [Google Scholar]
  56. Chen X, Ding Y, Yang Y, Song C, Wang B, Yang S, Guo Y, Gong Z. Protein kinases in plant responses to drought, salt, and cold stress. J Integr Plant Biol. 2021;63:53–78. doi: 10.1111/jipb.13061. [DOI] [PubMed] [Google Scholar]
  57. Chen ZJ, Sreedasyam A, Ando A, Song Q, De Santiago LM, Hulse-Kemp AM, Ding M, Ye W, Kirkbride RC, Jenkins J, et al. Genomic diversifications of five Gossypium allopolyploid species and their impact on cotton improvement. Nat Genet. 2020;52:525–533. doi: 10.1038/s41588-020-0614-5. [DOI] [PMC free article] [PubMed] [Google Scholar]
  58. Cheng X, Wang A. Multifaceted defense and counter-defense in co-evolutionary arms race between plants and viruses. Commun Integr Biol. 2017;10:e1341025. doi: 10.1080/19420889.2017.1341025. [DOI] [Google Scholar]
  59. Cheviron ZA, Bachman GC, Connaty AD, McClelland GB, Storz JF. Regulatory changes contribute to the adaptive enhancement of thermogenic capacity in high-altitude deer mice. Proc Natl Acad Sci USA. 2012;109:8635–8640. doi: 10.1073/pnas.1120523109. [DOI] [PMC free article] [PubMed] [Google Scholar]
  60. Chikina M, Robinson JD, Clark NL. Hundreds of genes experienced convergent shifts in selective pressure in marine mammals. Mol Biol Evol. 2016;33:2182–2192. doi: 10.1093/molbev/msw112. [DOI] [PMC free article] [PubMed] [Google Scholar]
  61. Chitwood DH, Sinha NR. Evolutionary and environmental forces sculpting leaf development. Curr Biol. 2016;26:R297–R306. doi: 10.1016/j.cub.2016.02.033. [DOI] [PubMed] [Google Scholar]
  62. Christin PA, Salamin N, Muasya AM, Roalson EH, Russier F, Besnard G. Evolutionary switch and genetic convergence on rbcL following the evolution of C4 photosynthesis. Mol Biol Evol. 2008;25:2361–2368. doi: 10.1093/molbev/msn178. [DOI] [PubMed] [Google Scholar]
  63. Christin PA, Salamin N, Savolainen V, Duvall MR, Besnard G. C4 photosynthesis evolved in grasses via parallel adaptive genetic changes. Curr Biol. 2007;17:1241–1247. doi: 10.1016/j.cub.2007.06.036. [DOI] [PubMed] [Google Scholar]
  64. Christin PA, Weinreich DM, Besnard G. Causes and evolutionary significance of genetic convergence. Trends Genet. 2010;26:400–405. doi: 10.1016/j.tig.2010.06.005. [DOI] [PubMed] [Google Scholar]
  65. Clark RM, Schweikert G, Toomajian C, Ossowski S, Zeller G, Shinn P, Warthmann N, Hu TT, Fu G, Hinds DA, et al. Common sequence polymorphisms shaping genetic diversity in Arabidopsis thaliana. Science. 2007;317:338–342. doi: 10.1126/science.1138632. [DOI] [PubMed] [Google Scholar]
  66. Clayton DH, Bush SE, Goates BM, Johnson KP. Host defense reinforces host-parasite cospeciation. Proc Natl Acad Sci USA. 2003;100:15694–15699. doi: 10.1073/pnas.2533751100. [DOI] [PMC free article] [PubMed] [Google Scholar]
  67. Cogni R, Cao C, Day JP, Bridson C, Jiggins FM. The genetic architecture of resistance to virus infection in Drosophila. Mol Ecol. 2016;25:5228–5241. doi: 10.1111/mec.13769. [DOI] [PMC free article] [PubMed] [Google Scholar]
  68. Cohen C, Liltved WR, Colville JF, Shuttleworth A, Weissflog J, Svatoš A, Bytebier B, Johnson SD. Sexual deception of a beetle pollinator through floral mimicry. Curr Biol. 2021;31:1962–1969.e6. doi: 10.1016/j.cub.2021.03.037. [DOI] [PubMed] [Google Scholar]
  69. Conn CE, Bythell-Douglas R, Neumann D, Yoshida S, Whittington B, Westwood JH, Shirasu K, Bond CS, Dyer KA, Nelson D C. Convergent evolution of strigolactone perception enabled host detection in parasitic plants. Science. 2015;349:540–543. doi: 10.1126/science.aab1140. [DOI] [PubMed] [Google Scholar]
  70. Cook JM, Rasplus JY. Mutualists with attitude: coevolving fig wasps and figs. Trends Ecol Evol. 2003;18:241–248. doi: 10.1016/S0169-5347(03)00062-4. [DOI] [Google Scholar]
  71. Cook JM, West SA. Figs and fig wasps. Curr Biol. 2005;15:R978–R980. doi: 10.1016/j.cub.2005.11.057. [DOI] [PubMed] [Google Scholar]
  72. Cooper LN, Berta A, Dawson SD, Reidenberg JS. Evolution of hyperphalangy and digit reduction in the cetacean manus. Anat Rec. 2007;290:654–672. doi: 10.1002/ar.20532. [DOI] [PubMed] [Google Scholar]
  73. Cosby RL, Judd J, Zhang R, Zhong A, Garry N, Pritham EJ, Feschotte C. Recurrent evolution of vertebrate transcription factors by transposase capture. Science. 2021;371:eabc6405. doi: 10.1126/science.abc6405. [DOI] [PMC free article] [PubMed] [Google Scholar]
  74. Dagoneau N, Goulet M, Geneviève D, Sznajer Y, Martinovic J, Smithson S, Huber C, Baujat G, Flori E, Tecco L, et al. DYNC2H1 mutations cause asphyxiating thoracic dystrophy and short rib-polydactyly syndrome, type III. Am J Hum Genet. 2009;84:706–711. doi: 10.1016/j.ajhg.2009.04.016. [DOI] [PMC free article] [PubMed] [Google Scholar]
  75. D’Alessandro A, Nemkov T, Bogren LK, Martin SL, Hansen K C. Comfortably Numb and Back: plasma metabolomics reveals biochemical adaptations in the hibernating 13-lined ground squirrel. J Proteome Res. 2017;16:958–969. doi: 10.1021/acs.jproteome.6b00884. [DOI] [PubMed] [Google Scholar]
  76. Dallos P, Fakler B. Prestin, a new type of motor protein. Nat Rev Mol Cell Biol. 2002;3:104–111. doi: 10.1038/nrm730. [DOI] [PubMed] [Google Scholar]
  77. Darwin CR. On the Various Contrivances by Which British and Foreign Orchids are Fertilised by Insects, and on the Good Effects Of Intercrossing. London: John Murray; 1862. [PMC free article] [PubMed] [Google Scholar]
  78. Davies KT, Tsagkogeorga G, Rossiter SJ. Divergent evolutionary rates in vertebrate and mammalian specific conserved non-coding elements (CNEs) in echolocating mammals. BMC Evol Biol. 2014;14:261. doi: 10.1186/s12862-014-0261-5. [DOI] [PMC free article] [PubMed] [Google Scholar]
  79. Davies KTJ, Bennett NC, Faulkes CG, Rossiter SJ. Limited evidence for parallel molecular adaptations associated with the subterranean niche in mammals: a comparative study of three superorders. Mol Biol Evol. 2018;35:2544–2559. doi: 10.1093/molbev/msy161. [DOI] [PMC free article] [PubMed] [Google Scholar]
  80. Davis AP, Capecchi MR. Axial homeosis and appendicular skeleton defects in mice with a targeted disruption of hoxd-11. Development. 1994;120:2187–2198. doi: 10.1242/dev.120.8.2187. [DOI] [PubMed] [Google Scholar]
  81. Davis CC, Xi Z. Horizontal gene transfer in parasitic plants. Curr Opin Plant Biol. 2015;26:14–19. doi: 10.1016/j.pbi.2015.05.008. [DOI] [PubMed] [Google Scholar]
  82. De Bellocq JG, Charbonnel N, Morand S. Coevolutionary relationship between helminth diversity and MHC class II polymorphism in rodents. J Evolary Biol. 2008;21:1144–1150. doi: 10.1111/j.1420-9101.2008.01538.x. [DOI] [PubMed] [Google Scholar]
  83. Delsuc F, Metcalf JL, Wegener Parfrey L, Song SJ, González A, Knight R. Convergence of gut microbiomes in myrmecophagous mammals. Mol Ecol. 2014;23:1301–1317. doi: 10.1111/mec.12501. [DOI] [PubMed] [Google Scholar]
  84. Demuth JP, Bie TD, Stajich JE, Cristianini N, Hahn MW. The evolution of mammalian gene families. PLoS ONE. 2006;1:e85. doi: 10.1371/journal.pone.0000085. [DOI] [PMC free article] [PubMed] [Google Scholar]
  85. Deng XG, Wang K, Zhang SD, Su JP, Zhang TZ, Lin GH. Transcriptomatic determination of convergent evolution between plateau zokors (Eospalax baileyi) and naked mole rats (Heterocephalus glaber) Acta Theriol Sin. 2014;34:129–137. [Google Scholar]
  86. Denoeud F, Carretero-Paulet L, Dereeper A, Droc G, Guyot R, Pietrella M, Zheng C, Alberti A, Anthony F, Aprea G, et al. The coffee genome provides insight into the convergent evolution of caffeine biosynthesis. Science. 2014;345:1181–1184. doi: 10.1126/science.1255274. [DOI] [PubMed] [Google Scholar]
  87. Dhaka A, Viswanath V, Patapoutian A. Trp ion channels and temperature sensation. Annu Rev Neurosci. 2006;29:135–161. doi: 10.1146/annurev.neuro.29.051605.112958. [DOI] [PubMed] [Google Scholar]
  88. Ding SW. RNA-based antiviral immunity. Nat Rev Immunol. 2010;10:632–644. doi: 10.1038/nri2824. [DOI] [PubMed] [Google Scholar]
  89. Dobler S, Dalla S, Wagschal V, Agrawal AA. Community-wide convergent evolution in insect adaptation to toxic cardenolides by substitutions in the Na,K-ATPase. Proc Natl Acad Sci USA. 2012;109:13040–13045. doi: 10.1073/pnas.1202111109. [DOI] [PMC free article] [PubMed] [Google Scholar]
  90. Domb LG, Pagel M. Sexual swellings advertise female quality in wild baboons. Nature. 2001;410:204–206. doi: 10.1038/35065597. [DOI] [PubMed] [Google Scholar]
  91. Domínguez M, Dugas E, Benchouaia M, Leduque B, Jiménez-Gómez JM, Colot V, Quadrana L. The impact of transposable elements on tomato diversity. Nat Commun. 2020;11:4058. doi: 10.1038/s41467-020-17874-2. [DOI] [PMC free article] [PubMed] [Google Scholar]
  92. Doolittle RF. Convergent evolution: the need to be explicit. Trends Biochem Sci. 1994;19:15–18. doi: 10.1016/0968-0004(94)90167-8. [DOI] [PubMed] [Google Scholar]
  93. Dorone Y, Boeynaems S, Flores E, Jin B, Hateley S, Bossi F, Lazarus E, Pennington JG, Michiels E, De Decker M, et al. A prion-like protein regulator of seed germination undergoes hydration-dependent phase separation. Cell. 2021;184:4284–4298.e27. doi: 10.1016/j.cell.2021.06.009. [DOI] [PMC free article] [PubMed] [Google Scholar]
  94. Duan Y, Dou S, Porath HT, Huang J, Eisenberg E, Lu J. A-to-I RNA editing in honeybees shows signals of adaptation and convergent evolution. iScience. 2021;24:101983. doi: 10.1016/j.isci.2020.101983. [DOI] [PMC free article] [PubMed] [Google Scholar]
  95. Dubost G. Les mammifères souterrains. Rev Ecol Biol Sol. 1968;5:99–133. [Google Scholar]
  96. Duke NC. Mangrove floristics and biogeography. American Geophysical Union. 1992;41:63–100. [Google Scholar]
  97. Durvasula A, Fulgione A, Gutaker RM, Alacakaptan SI, Flood PJ, Neto C, Tsuchimatsu T, Burbano HA, Picó FX, Alonso-Blanco C, et al. African genomes illuminate the early history and transition to selfing in Arabidopsis thaliana. Proc Natl Acad Sci USA. 2017;114:5213–5218. doi: 10.1073/pnas.1616736114. [DOI] [PMC free article] [PubMed] [Google Scholar]
  98. Edger PP, Pires JC. Gene and genome duplications: the impact of dosage-sensitivity on the fate of nuclear genes. Chromosome Res. 2009;17:699–717. doi: 10.1007/s10577-009-9055-9. [DOI] [PubMed] [Google Scholar]
  99. Ehrlich PR, Raven PH. Butterflies and plants: a study in coevolution. Evolution. 1964;18:586–608. doi: 10.2307/2406212. [DOI] [Google Scholar]
  100. Eimer H, Sureshkumar S, Singh Yadav A, Kraupner-Taylor C, Bandaranayake C, Seleznev A, Thomason T, Fletcher SJ, Gordon SF, Carroll BJ, et al. RNA-dependent epigenetic silencing directs transcriptional downregulation caused by intronic repeat expansions. Cell. 2018;174:1095–1105.e11. doi: 10.1016/j.cell.2018.06.044. [DOI] [PubMed] [Google Scholar]
  101. Eizirik E, Trindade FJ. Genetics and evolution of mammalian coat pigmentation. Annu Rev Anim Biosci. 2021;9:125–148. doi: 10.1146/annurev-animal-022114-110847. [DOI] [PubMed] [Google Scholar]
  102. Eizirik E, Murphy WJ, Koepfli KP, Johnson WE, Dragoo JW, Wayne RK, O’Brien SJ. Pattern and timing of diversification of the mammalian order Carnivora inferred from multiple nuclear gene sequences. Mol Phylogenet Evol. 2010;56:49–63. doi: 10.1016/j.ympev.2010.01.033. [DOI] [PMC free article] [PubMed] [Google Scholar]
  103. Eizirik E, Yuhki N, Johnson WE, Menotti-Raymond M, Hannah SS, O’Brien SJ. Molecular genetics and evolution of melanism in the cat family. Curr Biol. 2003;13:448–453. doi: 10.1016/S0960-9822(03)00128-3. [DOI] [PubMed] [Google Scholar]
  104. Elith J, Leathwick JR. Species distribution models: ecological explanation and prediction across space and time. Annu Rev Ecol Evol Syst. 2009;40:677–697. doi: 10.1146/annurev.ecolsys.110308.120159. [DOI] [Google Scholar]
  105. Emms DM, Covshoff S, Hibberd JM, Kelly S. Independent and parallel evolution of new genes by gene duplication in two origins of C4 photosynthesis provides new insight into the mechanism of phloem loading in C4 species. Mol Biol Evol. 2016;33:1796–1806. doi: 10.1093/molbev/msw057. [DOI] [PMC free article] [PubMed] [Google Scholar]
  106. Endoh-Yamagami S, Karkar KM, May SR, Cobos I, Thwin MT, Long JE, Ashique AM, Zarbalis K, Rubenstein JLR, Peterson AS. A mutation in the pericentrin gene causes abnormal interneuron migration to the olfactory bulb in mice. Dev Biol. 2010;340:41–53. doi: 10.1016/j.ydbio.2010.01.017. [DOI] [PubMed] [Google Scholar]
  107. Estep MC, McKain MR, Vela Diaz D, Zhong J, Hodge JG, Hodkinson TR, Layton DJ, Malcomber ST, Pasquet R, Kellogg EA. Allopolyploidy, diversification, and the Miocene grassland expansion. Proc Natl Acad Sci USA. 2014;111:15149–15154. doi: 10.1073/pnas.1404177111. [DOI] [PMC free article] [PubMed] [Google Scholar]
  108. Evans LM, Slavov GT, Rodgers-Melnick E, Martin J, Ranjan P, Muchero W, Brunner AM, Schackwitz W, Gunter L, Chen JG, et al. Population genomics of Populus trichocarpa identifies signatures of selection and adaptive trait associations. Nat Genet. 2014;46:1089–1096. doi: 10.1038/ng.3075. [DOI] [PubMed] [Google Scholar]
  109. Exposito-Alonso M, Burbano HA, Bossdorf O, Nielsen R, Weigel D. Natural selection on the Arabidopsis thaliana genome in present and future climates. Nature. 2019;573:126–129. doi: 10.1038/s41586-019-1520-9. [DOI] [PubMed] [Google Scholar]
  110. Ezenwa VO, Gerardo NM, Inouye DW, Medina M, Xavier JB. Animal behavior and the microbiome. Science. 2012;338:198–199. doi: 10.1126/science.1227412. [DOI] [PubMed] [Google Scholar]
  111. Fan H, Chen L, Hu Y, Shi G, Dai Y, Wei F, Wu Q. A whole-genome association approach for large-scale interspecies traits. Sci China Life Sci. 2021;64:1372–1374. doi: 10.1007/s11427-020-1771-5. [DOI] [PubMed] [Google Scholar]
  112. Favier B, Le Meur M, Chambon P, Dolle P. Axial skeleton homeosis and forelimb malformations in Hoxd-11 mutant mice. Proc Natl Acad Sci USA. 1995;92:310–314. doi: 10.1073/pnas.92.1.310. [DOI] [PMC free article] [PubMed] [Google Scholar]
  113. Feldman CR, Brodie Edmund D, J, Brodie Edmund D, I, Pfrender ME. The evolutionary origins of beneficial alleles during the repeated adaptation of garter snakes to deadly prey. Proc Natl Acad Sci USA. 2009;106:13415–13420. doi: 10.1073/pnas.0901224106. [DOI] [PMC free article] [PubMed] [Google Scholar]
  114. Feldman CR, Brodie ED, Jr, Brodie Iii ED, Pfrender ME. Genetic architecture of a feeding adaptation: garter snake (Thamnophis) resistance to tetrodotoxin bearing prey. Proc R Soc B. 2010;277:3317–3325. doi: 10.1098/rspb.2010.0748. [DOI] [PMC free article] [PubMed] [Google Scholar]
  115. Feng C, Liu R, Xu W, Zhou Y, Zhu C, Liu J, Wu B, Li Y, Qiu Q, He S, et al. The genome of a new anemone species (Actiniaria: Hormathiidae) provides insights into deep-sea adaptation. Deep Sea Res Part I. 2021;170:103492. doi: 10.1016/j.dsr.2021.103492. [DOI] [Google Scholar]
  116. Feng P, Zheng J, Rossiter SJ, Wang D, Zhao H. Massive losses of taste receptor genes in toothed and baleen whales. Genome Biol Evol. 2014;6:1254–1265. doi: 10.1093/gbe/evu095. [DOI] [PMC free article] [PubMed] [Google Scholar]
  117. Feng S, Bai M, Rivas-González I, Li C, Liu S, Tong Y, Yang H, Chen G, Xie D, Sears KE, et al. Incomplete lineage sorting and phenotypic evolution in marsupials. Cell. 2022;185:1646–1660.e18. doi: 10.1016/j.cell.2022.03.034. [DOI] [PMC free article] [PubMed] [Google Scholar]
  118. Feng X, Li G, Xu S, Wu W, Chen Q, Shao S, Liu M, Wang N, Zhong C, He Z, et al. Genomic insights into molecular adaptation to intertidal environments in the mangrove Aegiceras corniculatum. New Phytol. 2021;231:2346–2358. doi: 10.1111/nph.17551. [DOI] [PubMed] [Google Scholar]
  119. Figueiró HV, Li G, Trindade FJ, Assis J, Pais F, Fernandes G, Santos SHD, Hughes GM, Komissarov A, Antunes A, et al. Genome-wide signatures of complex introgression and adaptive evolution in the big cats. Sci Adv. 2017;3:e1700299. doi: 10.1126/sciadv.1700299. [DOI] [PMC free article] [PubMed] [Google Scholar]
  120. Fine PVA, Mesones I, Coley PD. Herbivores promote habitat specialization by trees in Amazonian forests. Science. 2004;305:663–665. doi: 10.1126/science.1098982. [DOI] [PubMed] [Google Scholar]
  121. Fitzpatrick MC, Keller SR. Ecological genomics meets community-level modelling of biodiversity: mapping the genomic landscape of current and future environmental adaptation. Ecol Lett. 2015;18:1–16. doi: 10.1111/ele.12376. [DOI] [PubMed] [Google Scholar]
  122. Flowers TJ, Galal HK, Bromham L. Evolution of halophytes: multiple origins of salt tolerance in land plants. Funct Plant Biol. 2010;37:604–612. doi: 10.1071/FP09269. [DOI] [Google Scholar]
  123. Foote AD, Liu Y, Thomas GWC, Vinař T, Alföldi J, Deng J, Dugan S, van Elk CE, Hunter ME, Joshi V, et al. Convergent evolution of the genomes of marine mammals. Nat Genet. 2015;47:272–275. doi: 10.1038/ng.3198. [DOI] [PMC free article] [PubMed] [Google Scholar]
  124. Fournier-Level A, Korte A, Cooper MD, Nordborg M, Schmitt J, Wilczek AM. A map of local adaptation in Arabidopsis thaliana. Science. 2011;334:86–89. doi: 10.1126/science.1209271. [DOI] [PubMed] [Google Scholar]
  125. Fraile A, García-Arenal F. The coevolution of plants and viruses: resistance and pathogenicity. Adv Virus Res. 2010;76:1–32. doi: 10.1016/S0065-3527(10)76001-2. [DOI] [PubMed] [Google Scholar]
  126. Franche C, Lindström K, Elmerich C. Nitrogen-fixing bacteria associated with leguminous and non-leguminous plants. Plant Soil. 2009;321:35–59. doi: 10.1007/s11104-008-9833-8. [DOI] [Google Scholar]
  127. Fu H, Jiao Z, Li Y, Tian J, Ren L, Zhang F, Li Q, Liu S. Transient receptor potential (trp) channels in the pacific oyster (Crassostrea gigas): genome-wide identification and expression profiling after heat stress between C. gigas and C. angulata. Int J Mol Sci. 2021;22:3222. doi: 10.3390/ijms22063222. [DOI] [PMC free article] [PubMed] [Google Scholar]
  128. Fukushima K, Fang X, Alvarez-Ponce D, Cai H, Carretero-Paulet L, Chen C, Chang TH, Farr KM, Fujita T, Hiwatashi Y, et al. Genome of the pitcher plant Cephalotus reveals genetic changes associated with carnivory. Nat Ecol Evol. 2017;1:1–9. doi: 10.1038/s41559-016-0059. [DOI] [PubMed] [Google Scholar]
  129. Funk ER, Mason NA, Pálsson S, Albrecht T, Johnson JA, Taylor SA. A supergene underlies linked variation in color and morphology in a Holarctic songbird. Nat Commun. 2021;12:6833. doi: 10.1038/s41467-021-27173-z. [DOI] [PMC free article] [PubMed] [Google Scholar]
  130. Futuyma DJ. Evolution. Third Edition. Oxford: Oxford University Press; 2013. [Google Scholar]
  131. Gao G, Xu M, Bai C, Yang Y, Li G, Xu J, Wei Z, Min J, Su G, Zhou X, et al. Comparative genomics and transcriptomics of Chrysolophus provide insights into the evolution of complex plumage colouration. GigaScience. 2018;7:giy113. doi: 10.1093/gigascience/giy113. [DOI] [PMC free article] [PubMed] [Google Scholar]
  132. Gaulke CA, Arnold HK, Humphreys IR, Kembel SW, O’Dwyer J P, Sharpton TJ. Ecophylogenetics clarifies the evolutionary association between mammals and their gut microbiota. mBio. 2018;9:e01348–18. doi: 10.1128/mBio.01348-18. [DOI] [PMC free article] [PubMed] [Google Scholar]
  133. Ge RL, Cai Q, Shen YY, San A, Ma L, Zhang Y, Yi X, Chen Y, Yang L, Huang Y, et al. Draft genome sequence of the Tibetan antelope. Nat Commun. 2013;4:1858. doi: 10.1038/ncomms2860. [DOI] [PMC free article] [PubMed] [Google Scholar]
  134. Genomes Consortium 1,135 genomes reveal the global pattern of polymorphism in Arabidopsis thaliana. Cell. 2016;166:481–491. doi: 10.1016/j.cell.2016.05.063. [DOI] [PMC free article] [PubMed] [Google Scholar]
  135. Gerald, W., Han, J., and Long, R. (2003). The Yak. FAO Regional Office for Asia and the Pacific.
  136. Gleadow RM, Möller BL. Cyanogenic glycosides: synthesis, physiology, and phenotypic plasticity. Annu Rev Plant Biol. 2014;65:155–185. doi: 10.1146/annurev-arplant-050213-040027. [DOI] [PubMed] [Google Scholar]
  137. Goerner-Potvin P, Bourque G. Computational tools to unmask transposable elements. Nat Rev Genet. 2018;19:688–704. doi: 10.1038/s41576-018-0050-x. [DOI] [PubMed] [Google Scholar]
  138. Goldstein RA, Pollard ST, Shah SD, Pollock DD. Nonadaptive amino acid convergence rates decrease over time. Mol Biol Evol. 2015;32:1373–1381. doi: 10.1093/molbev/msv041. [DOI] [PMC free article] [PubMed] [Google Scholar]
  139. Gong Z, Xiong L, Shi H, Yang S, Herrera-Estrella LR, Xu G, Chao DY, Li J, Wang PY, Qin F, et al. Plant abiotic stress response and nutrient use efficiency. Sci China Life Sci. 2020;63:635–674. doi: 10.1007/s11427-020-1683-x. [DOI] [PubMed] [Google Scholar]
  140. Gougherty AV, Keller SR, Fitzpatrick MC. Maladaptation, migration and extirpation fuel climate change risk in a forest tree species. Nat Clim Chang. 2021;11:166–171. doi: 10.1038/s41558-020-00968-6. [DOI] [Google Scholar]
  141. Grabek KR, Cooke TF, Epperson LE, Spees KK, Cabral GF, Sutton SC, Merriman DK, Martin SL, Bustamante CD. Genetic variation drives seasonal onset of hibernation in the 13-lined ground squirrel. Commun Biol. 2019;2:478. doi: 10.1038/s42003-019-0719-5. [DOI] [PMC free article] [PubMed] [Google Scholar]
  142. Grabek KR, Martin SL, Hindle AG. Proteomics approaches shed new light on hibernation physiology. J Comp Physiol B. 2015;185:607–627. doi: 10.1007/s00360-015-0905-9. [DOI] [PubMed] [Google Scholar]
  143. Grant PR, Abbott I. Interspecific competition, island biogeography and null hypotheses. Evolution. 1980;34:332–341. doi: 10.2307/2407397. [DOI] [PubMed] [Google Scholar]
  144. Grant PR, Grant BR, Markert JA, Keller LF, Petren K. Convergent evolution of Darwin’s finches caused by introgressive hybridization and selection. Evolution. 2004;58:1588–1599. doi: 10.1111/j.0014-3820.2004.tb01738.x. [DOI] [PubMed] [Google Scholar]
  145. Gravato-Nobre MJ, Nicholas HR, Nijland R, O’Rourke D, Whittington DE, Yook KJ, Hodgkin J. Multiple genes affect sensitivity of Caenorhabditis elegans to the bacterial pathogen Microbacterium nematophilum. Genetics. 2005;171:1033–1045. doi: 10.1534/genetics.105.045716. [DOI] [PMC free article] [PubMed] [Google Scholar]
  146. Greilhuber J. Intraspecific variation in genome size in angiosperms: identifying its existence. Ann Bot. 2005;95:91–98. doi: 10.1093/aob/mci004. [DOI] [PMC free article] [PubMed] [Google Scholar]
  147. Grosse J, Heffron H, Burling K, Akhter Hossain M, Habib AM, Rogers GJ, Richards P, Larder R, Rimmington D, Adriaenssens AA, et al. Insulin-like peptide 5 is an orexigenic gastrointestinal hormone. Proc Natl Acad Sci USA. 2014;111:11133–11138. doi: 10.1073/pnas.1411413111. [DOI] [PMC free article] [PubMed] [Google Scholar]
  148. Guimarães PR, Jr, Jordano P, Thompson JN. Evolution and coevolution in mutualistic networks. Ecol Lett. 2011;14:877–885. doi: 10.1111/j.1461-0248.2011.01649.x. [DOI] [PubMed] [Google Scholar]
  149. Gujas B, Alonso-Blanco C, Hardtke CS. Natural Arabidopsis brx loss-of-function alleles confer root adaptation to acidic soil. Curr Biol. 2012;22:1962–1968. doi: 10.1016/j.cub.2012.08.026. [DOI] [PubMed] [Google Scholar]
  150. Guo YL. Gene family evolution in green plants with emphasis on the origination and evolution of Arabidopsis thaliana genes. Plant J. 2013;73:941–951. doi: 10.1111/tpj.12089. [DOI] [PubMed] [Google Scholar]
  151. Guo YL, Todesco M, Hagmann J, Das S, Weigel D. Independent FLC mutations as causes of flowering-time variation in Arabidopsis thaliana and Capsella rubella. Genetics. 2012;192:729–739. doi: 10.1534/genetics.112.143958. [DOI] [PMC free article] [PubMed] [Google Scholar]
  152. Guo YL, Zhao X, Lanz C, Weigel D. Evolution of the S-locus region in Arabidopsis relatives. Plant Physiol. 2011;157:937–946. doi: 10.1104/pp.111.174912. [DOI] [PMC free article] [PubMed] [Google Scholar]
  153. Hafner MS, Nadler SA. Cospeciation in host-parasite assemblages: comparative analysis of rates of evolution and timing of cospeciation events. Syst Zool. 1990;39:192–204. doi: 10.2307/2992181. [DOI] [Google Scholar]
  154. Hahn MW, Han MV, Han S-G. Gene family evolution across 12 Drosophila genomes. PLoS Genet. 2007;3:e197. doi: 10.1371/journal.pgen.0030197. [DOI] [PMC free article] [PubMed] [Google Scholar]
  155. Han TS, Wu Q, Hou XH, Li ZW, Zou YP, Ge S, Guo YL. Frequent introgressions from diploid species contribute to the adaptation of the tetraploid shepherd’s purse (Capsella bursa-pastoris) Mol Plant. 2015;8:427–438. doi: 10.1016/j.molp.2014.11.016. [DOI] [PubMed] [Google Scholar]
  156. Hancock AM, Brachi B, Faure N, Horton MW, Jarymowycz LB, Sperone FG, Toomajian C, Roux F, Bergelson J. Adaptation to climate across the Arabidopsis thaliana genome. Science. 2011;334:83–86. doi: 10.1126/science.1209244. [DOI] [PubMed] [Google Scholar]
  157. Hang R, Wang Z, Deng X, Liu C, Yan B, Yang C, Song X, Mo B, Cao X. Ribosomal RNA biogenesis and its response to chilling stress in Oryza sativa. Plant Physiol. 2018;177:381–397. doi: 10.1104/pp.17.01714. [DOI] [PMC free article] [PubMed] [Google Scholar]
  158. Hao Y, Xiong Y, Cheng Y, Song G, Jia C, Qu Y, Lei F. Comparative transcriptomics of 3 high-altitude passerine birds and their low-altitude relatives. Proc Natl Acad Sci USA. 2019;116:11851–11856. doi: 10.1073/pnas.1819657116. [DOI] [PMC free article] [PubMed] [Google Scholar]
  159. Hartmann FE, Rodríguez de la Vega RC, Carpentier F, Gladieux P, Cornille A, Hood ME, Giraud T. Understanding adaptation, coevolution, host specialization, and mating system in castrating anther-smut fungi by combining population and comparative genomics. Annu Rev Phytopathol. 2019;57:431–457. doi: 10.1146/annurev-phyto-082718-095947. [DOI] [PubMed] [Google Scholar]
  160. Hart T, Chandrashekhar M, Aregger M, Steinhart Z, Brown KR, MacLeod G, Mis M, Zimmermann M, Fradet-Turcotte A, Sun S, et al. High-resolution CRISPR screens reveal fitness genes and genotype-specific cancer liabilities. Cell. 2015;163:1515–1526. doi: 10.1016/j.cell.2015.11.015. [DOI] [PubMed] [Google Scholar]
  161. Hayashi T, Bohman B, Scaffidi A, Peakall R, Flematti GR. An unusual tricosatriene is crucial for male fungus gnat attraction and exploitation by sexually deceptive Pterostylis orchids. Curr Biol. 2021;31:1954–1961.e7. doi: 10.1016/j.cub.2021.01.095. [DOI] [PubMed] [Google Scholar]
  162. He F, Pasam R, Shi F, Kant S, Keeble-Gagnere G, Kay P, Forrest K, Fritz A, Hucl P, Wiebe K, et al. Exome sequencing highlights the role of wild-relative introgression in shaping the adaptive landscape of the wheat genome. Nat Genet. 2019;51:896–904. doi: 10.1038/s41588-019-0382-2. [DOI] [PubMed] [Google Scholar]
  163. He K, Liu Q, Xu DM, Qi FY, Bai J, He SW, Chen P, Zhou X, Cai WZ, Chen ZZ, et al. Echolocation in soft-furred tree mice. Science. 2021;372:eaay1513. doi: 10.1126/science.aay1513. [DOI] [PubMed] [Google Scholar]
  164. He Z, Feng X, Chen Q, Li L, Li S, Han K, Guo Z, Wang J, Liu M, Shi C, et al. Evolution of coastal forests based on a full set of mangrove genomes. Nat Ecol Evol. 2022;6:738–749. doi: 10.1038/s41559-022-01744-9. [DOI] [PubMed] [Google Scholar]
  165. He Z, Xu S, Zhang Z, Guo W, Lyu H, Zhong C, Boufford DE, Duke NC, Shi S. Convergent adaptation of the genomes of woody plants at the land-sea interface. Natl Sci Rev. 2020;7:978–993. doi: 10.1093/nsr/nwaa027. [DOI] [PMC free article] [PubMed] [Google Scholar]
  166. Hecker N, Sharma V, Hiller M. Convergent gene losses illuminate metabolic and physiological changes in herbivores and carnivores. Proc Natl Acad Sci USA. 2019;116:3036–3041. doi: 10.1073/pnas.1818504116. [DOI] [PMC free article] [PubMed] [Google Scholar]
  167. Hepworth J, Dean C. Flowering locus C’s lessons: conserved chromatin switches underpinning developmental timing and adaptation. Plant Physiol. 2015;168:1237–1245. doi: 10.1104/pp.15.00496. [DOI] [PMC free article] [PubMed] [Google Scholar]
  168. Herre EA, Jandér KC, Machado CA. Evolutionary ecology of figs and their associates: recent progress and outstanding puzzles. Annu Rev Ecol Evol Syst. 2008;39:439–458. doi: 10.1146/annurev.ecolsys.37.091305.110232. [DOI] [Google Scholar]
  169. Hetem RS, de Witt BA, Fick LG, Fuller A, Kerley GIH, Meyer L CR, Mitchell D, Maloney SK. Body temperature, thermoregulatory behaviour and pelt characteristics of three colour morphs of springbok (Antidorcas marsupialis) Comp Biochem Physiol Part A. 2009;152:379–388. doi: 10.1016/j.cbpa.2008.11.011. [DOI] [PubMed] [Google Scholar]
  170. Heyduk K, Moreno-Villena JJ, Gilman IS, Christin PA, Edwards EJ. The genetics of convergent evolution: insights from plant photosynthesis. Nat Rev Genet. 2019;20:485–493. doi: 10.1038/s41576-019-0107-5. [DOI] [PubMed] [Google Scholar]
  171. Hidalgo O, Pellicer J, Christenhusz M, Schneider H, Leitch AR, Leitch IJ. Is there an upper limit to genome size? Trends Plant Sci. 2017;22:567–573. doi: 10.1016/j.tplants.2017.04.005. [DOI] [PubMed] [Google Scholar]
  172. Hoekstra HE. Genetics, development and evolution of adaptive pigmentation in vertebrates. Heredity. 2006;97:222–234. doi: 10.1038/sj.hdy.6800861. [DOI] [PubMed] [Google Scholar]
  173. Hoekstra HE, Hirschmann RJ, Bundey RA, Insel PA, Crossland JP. A single amino acid mutation contributes to adaptive beach mouse color pattern. Science. 2006;313:101–104. doi: 10.1126/science.1126121. [DOI] [PubMed] [Google Scholar]
  174. Hofreiter M, Schöneberg T. The genetic and evolutionary basis of colour variation in vertebrates. Cell Mol Life Sci. 2010;67:2591–2603. doi: 10.1007/s00018-010-0333-7. [DOI] [PMC free article] [PubMed] [Google Scholar]
  175. Holding ML, Biardi JE, Gibbs HL. Coevolution of venom function and venom resistance in a rattlesnake predator and its squirrel prey. Proc R Soc B. 2016;283:20152841. doi: 10.1098/rspb.2015.2841. [DOI] [PMC free article] [PubMed] [Google Scholar]
  176. Holzinger F, Frick C, Wink M. Molecular basis for the insensitivity of the Monarch (Danaus plexippus) to cardiac glycosides. FEBS Lett. 1992;314:477–480. doi: 10.1016/0014-5793(92)81530-Y. [DOI] [PubMed] [Google Scholar]
  177. Horscroft JA, Kotwica AO, Laner V, West JA, Hennis PJ, Levett DZH, Howard DJ, Fernandez BO, Burgess SL, Ament Z, et al. Metabolic basis to Sherpa altitude adaptation. Proc Natl Acad Sci USA. 2017;114:6382–6387. doi: 10.1073/pnas.1700527114. [DOI] [PMC free article] [PubMed] [Google Scholar]
  178. Hoy RR. Convergent evolution of hearing. Science. 2012;338:894–895. doi: 10.1126/science.1231169. [DOI] [PubMed] [Google Scholar]
  179. Huelsmann M, Hecker N, Springer MS, Gatesy J, Sharma V, Hiller M. Genes lost during the transition from land to water in cetaceans highlight genomic changes associated with aquatic adaptations. Sci Adv. 2019;5:eaaw6671. doi: 10.1126/sciadv.aaw6671. [DOI] [PMC free article] [PubMed] [Google Scholar]
  180. Hu Q, Ma Y, Mandáková T, Shi S, Chen C, Sun P, Zhang L, Feng L, Zheng Y, Feng X, et al. Genome evolution of the psammophyte Pugionium for desert adaptation and further speciation. Proc Natl Acad Sci USA. 2021;118:e2025711118. doi: 10.1073/pnas.2025711118. [DOI] [PMC free article] [PubMed] [Google Scholar]
  181. Hu TT, Pattyn P, Bakker EG, Cao J, Cheng JF, Clark RM, Fahlgren N, Fawcett JA, Grimwood J, Gundlach H, et al. The Arabidopsis lyrata genome sequence and the basis of rapid genome size change. Nat Genet. 2011;43:476–481. doi: 10.1038/ng.807. [DOI] [PMC free article] [PubMed] [Google Scholar]
  182. Hu Y, Wu Q, Ma S, Ma T, Shan L, Wang X, Nie Y, Ning Z, Yan L, Xiu Y, et al. Comparative genomics reveals convergent evolution between the bamboo-eating giant and red pandas. Proc Natl Acad Sci USA. 2017;114:1081–1086. doi: 10.1073/pnas.1613870114. [DOI] [PMC free article] [PubMed] [Google Scholar]
  183. Hu YB, Yu LJ, Fan HZ, Huang GP, Wu Q, Nie YG, Liu S, Yan L, Wei FW. Genomic signatures of coevolution between non-model mammals and parasitic roundworms. Mol Biol Evol. 2021;38:531–544. doi: 10.1093/molbev/msaa243. [DOI] [PMC free article] [PubMed] [Google Scholar]
  184. Hu Y, Sun S, Fan H, Zhou W, Wei F. Exploring marine endosymbiosis systems with omics techniques. Sci China Life Sci. 2021;64:1013–1016. doi: 10.1007/s11427-021-1925-1. [DOI] [PubMed] [Google Scholar]
  185. Hu Z, Sackton TB, Edwards SV, Liu JS. Bayesian detection of convergent rate changes of conserved noncoding elements on phylogenetic trees. Mol Biol Evol. 2019;36:1086–1100. doi: 10.1093/molbev/msz049. [DOI] [PMC free article] [PubMed] [Google Scholar]
  186. Huang G, Wang X, Hu Y, Wu Q, Nie Y, Dong J, Ding Y, Yan L, Wei F. Diet drives convergent evolution of gut microbiomes in bamboo-eating species. Sci China Life Sci. 2021;64:88–95. doi: 10.1007/s11427-020-1750-7. [DOI] [PubMed] [Google Scholar]
  187. Huang G, Wang L, Li J, Hou R, Wang M, Wang Z, Qu Q, Zhou W, Nie Y, Hu Y, et al. Seasonal shift of the gut microbiome synchronizes host peripheral circadian rhythm for physiological adaptation to a low-fat diet in the giant panda. Cell Rep. 2022;38:110203. doi: 10.1016/j.celrep.2021.110203. [DOI] [PubMed] [Google Scholar]
  188. Huang X, Kurata N, Wei X, Wang ZX, Wang A, Zhao Q, Zhao Y, Liu K, Lu H, Li W, et al. A map of rice genome variation reveals the origin of cultivated rice. Nature. 2012;490:497–501. doi: 10.1038/nature11532. [DOI] [PMC free article] [PubMed] [Google Scholar]
  189. Husnik F, Nikoh N, Koga R, Ross L, Duncan RP, Fujie M, Tanaka M, Satoh N, Bachtrog D, Wilson ACC, et al. Horizontal gene transfer from diverse bacteria to an insect genome enables a tripartite nested mealybug symbiosis. Cell. 2013;153:1567–1578. doi: 10.1016/j.cell.2013.05.040. [DOI] [PubMed] [Google Scholar]
  190. Matsumoto T, Wu JZ, Kanamori H, Katayose Y, Fujisawa M, Namiki N, Mizuno H, Yamamoto K, Antonio BA, Baba T, et al. The map-based sequence of the rice genome. Nature. 2005;436:793–800. doi: 10.1038/nature03895. [DOI] [PubMed] [Google Scholar]
  191. Jacobsen DJ, Raguso RA. Lingering effects of herbivory and plant defenses on pollinators. Curr Biol. 2018;28:R1164–R1169. doi: 10.1016/j.cub.2018.08.010. [DOI] [PubMed] [Google Scholar]
  192. Janzen DH. How to be a fig. Annu Rev Ecol Syst. 1979;10:13–51. doi: 10.1146/annurev.es.10.110179.000305. [DOI] [Google Scholar]
  193. Janzen DH. When is it coevolution? Evolution. 1980;34:611–612. doi: 10.2307/2408229. [DOI] [PubMed] [Google Scholar]
  194. Jiang P, Josue J, Li X, Glaser D, Li W, Brand JG, Margolskee RF, Reed DR, Beauchamp GK. Major taste loss in carnivorous mammals. Proc Natl Acad Sci USA. 2012;109:4956–4961. doi: 10.1073/pnas.1118360109. [DOI] [PMC free article] [PubMed] [Google Scholar]
  195. Jiao WB, Schneeberger K. Chromosome-level assemblies of multiple Arabidopsis genomes reveal hotspots of rearrangements with altered evolutionary dynamics. Nat Commun. 2020;11:989. doi: 10.1038/s41467-020-14779-y. [DOI] [PMC free article] [PubMed] [Google Scholar]
  196. Jin WT, Gernandt DS, Wehenkel C, Xia XM, Wei XX, Wang XQ. Phylogenomic and ecological analyses reveal the spatiotemporal evolution of global pines. Proc Natl Acad Sci USA. 2021;118:e2022302118. doi: 10.1073/pnas.2022302118. [DOI] [PMC free article] [PubMed] [Google Scholar]
  197. Johnston JS, Pepper AE, Hall AE, Chen ZJ, Hodnett G, Drabek J, Lopez R, P HJ. Evolution of genome size in Brassicaceae. Ann Bot. 2005;95:229–235. doi: 10.1093/aob/mci016. [DOI] [PMC free article] [PubMed] [Google Scholar]
  198. Jones G, Holderied MW. Bat echolocation calls: adaptation and convergent evolution. Proc R Soc B. 2007;274:905–912. doi: 10.1098/rspb.2006.0200. [DOI] [PMC free article] [PubMed] [Google Scholar]
  199. Kang J, Zhang H, Sun T, Shi Y, Wang J, Zhang B, Wang Z, Zhou Y, Gu H. Natural variation of C-repeat-binding factor (CBFs) genes is a major cause of divergence in freezing tolerance among a group of Arabidopsis thaliana populations along the Yangtze River in China. New Phytol. 2013;199:1069–1080. doi: 10.1111/nph.12335. [DOI] [PubMed] [Google Scholar]
  200. Karageorgi M, Groen SC, Sumbul F, Pelaez JN, Verster KI, Aguilar JM, Hastings AP, Bernstein SL, Matsunaga T, Astourian M, et al. Genome editing retraces the evolution of toxin resistance in the monarch butterfly. Nature. 2019;574:409–412. doi: 10.1038/s41586-019-1610-8. [DOI] [PMC free article] [PubMed] [Google Scholar]
  201. Karasov TL, Kniskern JM, Gao L, Deyoung BJ, Ding J, Dubiella U, Lastra RO, Nallu S, Roux F, Innes RW, et al. The long-term maintenance of a resistance polymorphism through diffuse interactions. Nature. 2014;512:436–440. doi: 10.1038/nature13439. [DOI] [PMC free article] [PubMed] [Google Scholar]
  202. Karasov WH, Douglas AE. Comparative digestive physiology. Compr Physiol. 2013;3:741–783. doi: 10.1002/cphy.c110054. [DOI] [PMC free article] [PubMed] [Google Scholar]
  203. Kawahara T, Kuwano Y, Teshima-Kondo S, Takeya R, Sumimoto H, Kishi K, Tsunawaki S, Hirayama T, Rokutan K. Role of nicotinamide adenine dinucleotide phosphate oxidase 1 in oxidative burst response to Toll-like receptor 5 signaling in large intestinal epithelial cells. J Immunol. 2004;172:3051–3058. doi: 10.4049/jimmunol.172.5.3051. [DOI] [PubMed] [Google Scholar]
  204. Kawakatsu T, Huang SC, Jupe F, Sasaki E, Schmitz RJ, Urich M A, Castanon R, Nery JR, Barragan C, He Y, et al. Epigenomic diversity in a global collection of Arabidopsis thaliana accessions. Cell. 2016;166:492–505. doi: 10.1016/j.cell.2016.06.044. [DOI] [PMC free article] [PubMed] [Google Scholar]
  205. Kelly LJ, Plumb WJ, Carey DW, Mason ME, Cooper ED, Crowther W, Whittemore AT, Rossiter SJ, Koch JL, Buggs RJA. Convergent molecular evolution among ash species resistant to the emerald ash borer. Nat Ecol Evol. 2020;4:1116–1128. doi: 10.1038/s41559-020-1209-3. [DOI] [PMC free article] [PubMed] [Google Scholar]
  206. Kim G, LeBlanc ML, Wafula EK, dePamphilis CW, Westwood JH. Genomic-scale exchange of mRNA between a parasitic plant and its hosts. Science. 2014;345:808–811. doi: 10.1126/science.1253122. [DOI] [PubMed] [Google Scholar]
  207. Kim S, Cho YS, Kim HM, Chung O, Kim H, Jho S, Seomun H, Kim J, Bang WY, Kim C, et al. Comparison of carnivore, omnivore, and herbivore mammalian genomes with a new leopard assembly. Genome Biol. 2016;17:211. doi: 10.1186/s13059-016-1071-4. [DOI] [PMC free article] [PubMed] [Google Scholar]
  208. Kinzey WG. Dietary and dental adaptations in the Pitheciinae. Am J Phys Anthropol. 1992;88:499–514. doi: 10.1002/ajpa.1330880406. [DOI] [PubMed] [Google Scholar]
  209. Kirkness EF, Haas BJ, Sun W, Braig HR, Perotti MA, Clark JM, Lee SH, Robertson HM, Kennedy RC, Elhaik E, et al. Genome sequences of the human body louse and its primary endosymbiont provide insights into the permanent parasitic lifestyle. Proc Natl Acad Sci USA. 2010;107:12168–12173. doi: 10.1073/pnas.1003379107. [DOI] [PMC free article] [PubMed] [Google Scholar]
  210. Kishida T, Kubota S, Shirayama Y, Fukami H. The olfactory receptor gene repertoires in secondary-adapted marine vertebrates: evidence for reduction of the functional proportions in cetaceans. Biol Lett. 2007;3:428–430. doi: 10.1098/rsbl.2007.0191. [DOI] [PMC free article] [PubMed] [Google Scholar]
  211. Kishida T, Suzuki M, Takayama A. Evolution of the alternative AQP2 gene: acquisition of a novel protein-coding sequence in dolphins. Mol PhyloGenet Evol. 2018;118:54–57. doi: 10.1016/j.ympev.2017.09.012. [DOI] [PubMed] [Google Scholar]
  212. Klein J, Sato A, Nikolaidis N. MHC, TSP, and the origin of species: from immunogenetics to evolutionary genetics. Annu Rev Genet. 2007;41:281–304. doi: 10.1146/annurev.genet.41.110306.130137. [DOI] [PubMed] [Google Scholar]
  213. Knight CA, Molinari NA, Petrov DA. The large genome constraint hypothesis: evolution, ecology and phenotype. Ann Bot. 2005;95:177–190. doi: 10.1093/aob/mci011. [DOI] [PMC free article] [PubMed] [Google Scholar]
  214. Koenig D, Hagmann J, Li R, Bemm F, Slotte T, Neuffer B, Wright SI, Weigel D. Long-term balancing selection drives evolution of immunity genes in Capsella. eLife. 2019;8:e43606. doi: 10.7554/eLife.43606. [DOI] [PMC free article] [PubMed] [Google Scholar]
  215. Krauss SL, Phillips RD, Karron JD, Johnson SD, Roberts DG, Hopper SD. Novel consequences of bird pollination for plant mating. Trends Plant Sci. 2017;22:395–410. doi: 10.1016/j.tplants.2017.03.005. [DOI] [PubMed] [Google Scholar]
  216. Kryvokhyzha D, Salcedo A, Eriksson MC, Duan T, Tawari N, Chen J, Guerrina M, Kreiner JM, Kent TV, Lagercrantz U, et al. Parental legacy, demography, and admixture influenced the evolution of the two subgenomes of the tetraploid Capsella bursapastoris (Brassicaceae) PLoS Genet. 2019;15:e1007949. doi: 10.1371/journal.pgen.1007949. [DOI] [PMC free article] [PubMed] [Google Scholar]
  217. Kuzmin E, VanderSluis B, Nguyen Ba AN, Wang W, Koch EN, Usaj M, Khmelinskii A, Usaj MM, van Leeuwen J, Kraus O, et al. Exploring whole-genome duplicate gene retention with complex genetic interaction analysis. Science. 2020;368:5667–5678. doi: 10.1126/science.aaz5667. [DOI] [PMC free article] [PubMed] [Google Scholar]
  218. Kvon EZ, Kamneva OK, Melo US, Barozzi I, Osterwalder M, Mannion BJ, Tissières V, Pickle CS, Plajzer-Frick I, Lee EA, et al. Progressive loss of function in a limb enhancer during snake evolution. Cell. 2016;167:633–642.e11. doi: 10.1016/j.cell.2016.09.028. [DOI] [PMC free article] [PubMed] [Google Scholar]
  219. Laanto E, Hoikkala V, Ravantti J, Sundberg LR. Long-term genomic coevolution of host-parasite interaction in the natural environment. Nat Commun. 2017;8:111. doi: 10.1038/s41467-017-00158-7. [DOI] [PMC free article] [PubMed] [Google Scholar]
  220. Lain E, Carnejac S, Escher P, Wilson MC, Lømo T, Gajendran N, Brenner HR. A novel role for embigin to promote sprouting of motor nerve terminals at the neuromuscular junction. J Biol Chem. 2009;284:8930–8939. doi: 10.1074/jbc.M809491200. [DOI] [PMC free article] [PubMed] [Google Scholar]
  221. Lamichhaney S, Berglund J, Almén MS, Maqbool K, Grabherr M, Martinez-Barrio A, Promerová M, Rubin CJ, Wang C, Zamani N, et al. Evolution of Darwin’s finches and their beaks revealed by genome sequencing. Nature. 2015;518:371–375. doi: 10.1038/nature14181. [DOI] [PubMed] [Google Scholar]
  222. Lamichhaney S, Han F, Berglund J, Wang C, Almén MS, Webster MT, Grant BR, Grant PR, Andersson L. A beak size locus in Darwin’s finches facilitated character displacement during a drought. Science. 2016;352:470–474. doi: 10.1126/science.aad8786. [DOI] [PubMed] [Google Scholar]
  223. Larter M, Dunbar-Wallis A, Berardi A E, Smith S D. Convergent evolution at the pathway level: Predictable regulatory changes during flower color transitions. Mol Biol Evol. 2018;35:2159–2169. doi: 10.1093/molbev/msy117. [DOI] [PubMed] [Google Scholar]
  224. Lawson LP, Petren K. The adaptive genomic landscape of beak morphology in Darwin’s finches. Mol Ecol. 2017;26:4978–4989. doi: 10.1111/mec.14166. [DOI] [PubMed] [Google Scholar]
  225. Lee HT, Golicz AA, Bayer PE, Severn-Ellis AA, Chan CKK, Batley J, Kendrick GA, Edwards D. Genomic comparison of two independent seagrass lineages reveals habitat-driven convergent evolution. J Exp Bot. 2018;69:3689–3702. doi: 10.1093/jxb/ery147. [DOI] [PMC free article] [PubMed] [Google Scholar]
  226. Lee JH, Lewis KM, Moural TW, Kirilenko B, Borgonovo B, Prange G, Koessl M, Huggenberger S, Kang CH, Hiller M. Molecular parallelism in fast-twitch muscle proteins in echolocating mammals. Sci Adv. 2018;4:eaat9660. doi: 10.1126/sciadv.aat9660. [DOI] [PMC free article] [PubMed] [Google Scholar]
  227. Leghari SJ, Wahocho NA, Laghari GM, Laghari AH, Bhabhan G M, Talpur KH, Ahmed T, Wahocho SA, Lashari AA. Role of nitrogen for plant growth and development: a review. Adv Environ Biol. 2016;10:209–219. [Google Scholar]
  228. Li G, Wang J, Rossiter SJ, Jones G, Zhang S. Accelerated FoxP2 evolution in echolocating bats. PLoS ONE. 2007;2:e900. doi: 10.1371/journal.pone.0000900. [DOI] [PMC free article] [PubMed] [Google Scholar]
  229. Li G, Wang J, Rossiter SJ, Jones G, Cotton JA, Zhang S. The hearing gene Prestin reunites echolocating bats. Proc Natl Acad Sci USA. 2008;105:13959–13964. doi: 10.1073/pnas.0802097105. [DOI] [PMC free article] [PubMed] [Google Scholar]
  230. Li G, Wei H, Bi J, Ding X, Li L, Xu S, Yang G, Ren W. Insights into dietary switch in cetaceans: evidence from molecular evolution of proteinases and lipases. J Mol Evol. 2020;88:521–535. doi: 10.1007/s00239-020-09952-2. [DOI] [PubMed] [Google Scholar]
  231. Li H, Wang L, Luo MC, Nie F, Zhou Y, McGuire PE, Distelfeld A, Dai XT, Song CP, Dvorak J. Recombination between homoeologous chromosomes induced in durum wheat by the Aegilops speltoides Su1-Ph1 suppressor. Theor Appl Genet. 2019;132:3265–3276. doi: 10.1007/s00122-019-03423-z. [DOI] [PubMed] [Google Scholar]
  232. Li J, Shang S, Fang N, Zhu Y, Zhang J, Irwin DM, Zhang S, Wang Z. Accelerated evolution of limb-related gene Hoxd11 in the common ancestor of cetaceans and ruminants (Cetruminantia) G3 Genes Genomes Genet. 2020;10:515–524. doi: 10.1534/g3.119.400512. [DOI] [PMC free article] [PubMed] [Google Scholar]
  233. Li L, Foster CM, Gan Q, Nettleton D, James MG, Myers AM, Wurtele ES. Identification of the novel protein QQS as a component of the starch metabolic network in Arabidopsis leaves. Plant J. 2009;58:485–498. doi: 10.1111/j.1365-313X.2009.03793.x. [DOI] [PubMed] [Google Scholar]
  234. Li M, Tian S, Jin L, Zhou G, Li Y, Zhang Y, Wang T, Yeung CK L, Chen L, Ma J, et al. Genomic analyses identify distinct patterns of selection in domesticated pigs and Tibetan wild boars. Nat Genet. 2013;45:1431–1438. doi: 10.1038/ng.2811. [DOI] [PubMed] [Google Scholar]
  235. Li X, Guo T, Mu Q, Li X, Yu J. Genomic and environmental determinants and their interplay underlying phenotypic plasticity. Proc Natl Acad Sci USA. 2018;115:6679–6684. doi: 10.1073/pnas.1718326115. [DOI] [PMC free article] [PubMed] [Google Scholar]
  236. Li Y, Liu Z, Shi P, Zhang J. The hearing gene Prestin unites echolocating bats and whales. Curr Biol. 2010;20:R55–R56. doi: 10.1016/j.cub.2009.11.042. [DOI] [PubMed] [Google Scholar]
  237. Li YY, Liu Z, Qi FY, Zhou X, Shi P. Functional effects of a retained ancestral polymorphism in Prestin. Mol Biol Evol. 2017;34:88–92. doi: 10.1093/molbev/msw222. [DOI] [PubMed] [Google Scholar]
  238. Li Z, Defoort J, Tasdighian S, Maere S, Van de Peer Y, De Smet R. Gene duplicability of core genes is highly consistent across all angiosperms. Plant Cell. 2016;28:326–344. doi: 10.1105/tpc.15.00877. [DOI] [PMC free article] [PubMed] [Google Scholar]
  239. Li ZW, Chen X, Wu Q, Hagmann J, Han TS, Zou YP, Ge S, Guo YL. On the origin of de novo genes in Arabidopsis thaliana populations. Genome Biol Evol. 2016;8:2190–2202. doi: 10.1093/gbe/evw164. [DOI] [PMC free article] [PubMed] [Google Scholar]
  240. Li ZW, Hou XH, Chen JF, Xu YC, Wu Q, Gonzalez J, Guo YL. Transposable elements contribute to the adaptation of Arabidopsis thaliana. Genome Biol Evol. 2018;10:2140–2150. doi: 10.1093/gbe/evy171. [DOI] [PMC free article] [PubMed] [Google Scholar]
  241. Liu F, Marquardt S, Lister C, Swiezewski S, Dean C. Targeted 3’ processing of antisense transcripts triggers Arabidopsis FLC chromatin silencing. Science. 2010;327:94–97. doi: 10.1126/science.1180278. [DOI] [PubMed] [Google Scholar]
  242. Liu N, Shen G, Xu Y, Liu H, Zhang J, Li S, Li J, Zhang C, Qi J, Wang L, et al. Extensive inter-plant protein transfer between Cuscuta parasites and their host plants. Mol Plant. 2020;13:573–585. doi: 10.1016/j.molp.2019.12.002. [DOI] [PubMed] [Google Scholar]
  243. Liu XL, Wang YK, Ouyang S, Zhu YY, Li W, Hong X, Xu HY, Zhu XP. Evolutionary conservation of transferrin genomic organization and expression characterization in seven freshwater turtles. Biochem Biophysl Res Commun. 2018;506:874–882. doi: 10.1016/j.bbrc.2018.10.168. [DOI] [PubMed] [Google Scholar]
  244. Liu Y, Du H, Li P, Shen Y, Peng H, Liu S, Zhou GA, Zhang H, Liu Z, Shi M, et al. Pan-genome of wild and cultivated soybeans. Cell. 2020;182:162–176.e13. doi: 10.1016/j.cell.2020.05.023. [DOI] [PubMed] [Google Scholar]
  245. Liu Z, Li GH, Huang JF, Murphy RW, Shi P. Hearing aid for vertebrates via multiple episodic adaptive events on prestin genes. Mol Biol Evol. 2012;29:2187–2198. doi: 10.1093/molbev/mss087. [DOI] [PubMed] [Google Scholar]
  246. Liu Z, Qi FY, Zhou X, Ren HQ, Shi P. Parallel sites implicate functional convergence of the hearing gene prestin among echolocating mammals. Mol Biol Evol. 2014;31:2415–2424. doi: 10.1093/molbev/msu194. [DOI] [PubMed] [Google Scholar]
  247. Lobell DB, Schlenker W, Costa-Roberts J. Climate trends and global crop production since 1980. Science. 2011;333:616–620. doi: 10.1126/science.1204531. [DOI] [PubMed] [Google Scholar]
  248. Long Q, Rabanal FA, Meng D, Huber CD, Farlow A, Platzer A, Zhang Q, Vilhjálmsson BJ, Korte A, Nizhynska V, et al. Massive genomic variation and strong selection in Arabidopsis thaliana lines from Sweden. Nat Genet. 2013;45:884–890. doi: 10.1038/ng.2678. [DOI] [PMC free article] [PubMed] [Google Scholar]
  249. Lopes-Marques M, Ruivo R, Alves LQ, Sousa N, Machado AM, Castro LFC. The singularity of Cetacea behavior parallels the complete inactivation of melatonin gene modules. Genes. 2019;10:121. doi: 10.3390/genes10020121. [DOI] [PMC free article] [PubMed] [Google Scholar]
  250. Losos JB. Convergence, adaptation, and constraint. Evolution. 2011;65:1827–1840. doi: 10.1111/j.1558-5646.2011.01289.x. [DOI] [PubMed] [Google Scholar]
  251. Lu LM, Mao LF, Yang T, Ye JF, Liu B, Li HL, Sun M, Miller J T, Mathews S, Hu HH, et al. Evolutionary history of the angiosperm flora of China. Nature. 2018;554:234–238. doi: 10.1038/nature25485. [DOI] [PubMed] [Google Scholar]
  252. Lu Q, Wang K, Lei F, Yu D, Zhao H. Penguins reduced olfactory receptor genes common to other waterbirds. Sci Rep. 2016;6:31671. doi: 10.1038/srep31671. [DOI] [PMC free article] [PubMed] [Google Scholar]
  253. Lucas BA, Lavi E, Shiue L, Cho H, Katzman S, Miyoshi K, Siomi MC, Carmel L, Ares M, Jr., Maquat LE. Evidence for convergent evolution of SINE-directed Staufen-mediated mRNA decay. Proc Natl Acad Sci USA. 2018;115:968–973. doi: 10.1073/pnas.1715531115. [DOI] [PMC free article] [PubMed] [Google Scholar]
  254. Luo J, Moss CF. Echolocating bats rely on audiovocal feedback to adapt sonar signal design. Proc Natl Acad Sci USA. 2017;114:10978–10983. doi: 10.1073/pnas.1711892114. [DOI] [PMC free article] [PubMed] [Google Scholar]
  255. Luo SX, Zhang LJ, Yuan S, Ma ZH, Zhang DX, Renner SS. The largest early-diverging angiosperm family is mostly pollinated by ovipositing insects and so are most surviving lineages of early angiosperms. Proc R Soc B. 2018;285:20172365. doi: 10.1098/rspb.2017.2365. [DOI] [PMC free article] [PubMed] [Google Scholar]
  256. Lyu H, He Z, Wu CI, Shi S. Convergent adaptive evolution in marginal environments: unloading transposable elements as a common strategy among mangrove genomes. New Phytol. 2018;217:428–438. doi: 10.1111/nph.14784. [DOI] [PubMed] [Google Scholar]
  257. Ma J, Pazos IM, Gai F. Microscopic insights into the protein-stabilizing effect of trimethylamine N-oxide (TMAO) Proc Natl Acad Sci USA. 2014;111:8476–8481. doi: 10.1073/pnas.1403224111. [DOI] [PMC free article] [PubMed] [Google Scholar]
  258. Ma T, Wang J, Zhou G, Yue Z, Hu Q, Chen Y, Liu B, Qiu Q, Wang Z, Zhang J, et al. Genomic insights into salt adaptation in a desert poplar. Nat Commun. 2013;4:2797. doi: 10.1038/ncomms3797. [DOI] [PubMed] [Google Scholar]
  259. Ma Y, Dai X, Xu Y, Luo W, Zheng X, Zeng D, Pan Y, Lin X, Liu H, Zhang D, et al. COLD1 confers chilling tolerance in rice. Cell. 2015;160:1209–1221. doi: 10.1016/j.cell.2015.01.046. [DOI] [PubMed] [Google Scholar]
  260. Macdonald AG. Life at High Pressure: in the Deep Sea and Other Environments. Heidelberg: Springer Nature; 2021. [Google Scholar]
  261. Machado CA, Robbins N, Gilbert MTP, Herre EA. Critical review of host specificity and its coevolutionary implications in the fig/fig-wasp mutualism. Proc Natl Acad Sci USA. 2005;102:6558–6565. doi: 10.1073/pnas.0501840102. [DOI] [PMC free article] [PubMed] [Google Scholar]
  262. Mahler DL, Weber MG, Wagner CE, Ingram T. Pattern and process in the comparative study of convergent evolution. Am Natist. 2017;190:S13–S28. doi: 10.1086/692648. [DOI] [PubMed] [Google Scholar]
  263. Mamidi S, Healey A, Huang P, Grimwood J, Jenkins J, Barry K, Sreedasyam A, Shu S, Lovell JT, Feldman M, et al. A genome resource for green millet Setaria viridis enables discovery of agronomically valuable loci. Nat Biotechnol. 2020;38:1203–1210. doi: 10.1038/s41587-020-0681-2. [DOI] [PMC free article] [PubMed] [Google Scholar]
  264. Mao H, Wang H, Liu S, Li Z, Yang X, Yan J, Li J, Tran LSP, Qin F. A transposable element in a NAC gene is associated with drought tolerance in maize seedlings. Nat Commun. 2015;6:8326. doi: 10.1038/ncomms9326. [DOI] [PMC free article] [PubMed] [Google Scholar]
  265. Mao L, Kawaide H, Higuchi T, Chen M, Miyamoto K, Hirata Y, Kimura H, Miyazaki S, Teruya M, Fujiwara K, et al. Genomic evidence for convergent evolution of gene clusters for momilactone biosynthesis in land plants. Proc Natl Acad Sci USA. 2020;117:12472–12480. doi: 10.1073/pnas.1914373117. [DOI] [PMC free article] [PubMed] [Google Scholar]
  266. Maquat LE. Short interspersed nuclear element (SINE)-mediated post-transcriptional effects on human and mouse gene expression: SINE-UP for active duty. Phil Trans R Soc B. 2020;375:20190344. doi: 10.1098/rstb.2019.0344. [DOI] [PMC free article] [PubMed] [Google Scholar]
  267. Maron JL, Agrawal AA, Schemske DW. Plant-herbivore coevolution and plant speciation. Ecology. 2019;100:e02704. doi: 10.1002/ecy.2704. [DOI] [PubMed] [Google Scholar]
  268. Marquis RJ, Salazar D, Baer C, Reinhardt J, Priest G, Barnett K. Ode to Ehrlich and Raven or how herbivorous insects might drive plant speciation. Ecology. 2016;97:2939–2951. doi: 10.1002/ecy.1534. [DOI] [PubMed] [Google Scholar]
  269. Martel C, Francke W, Ayasse M. The chemical and visual bases of the pollination of the Neotropical sexually deceptive orchid Telipogon peruvianus. New Phytol. 2019;223:1989–2001. doi: 10.1111/nph.15902. [DOI] [PubMed] [Google Scholar]
  270. Matos-Cruz V, Schneider ER, Mastrotto M, Merriman DK, Bagriantsev SN, Gracheva EO. Molecular prerequisites for diminished cold sensitivity in ground squirrels and hamsters. Cell Rep. 2017;21:3329–3337. doi: 10.1016/j.celrep.2017.11.083. [DOI] [PMC free article] [PubMed] [Google Scholar]
  271. McCutcheon JP, von Dohlen CD. An interdependent metabolic patchwork in the nested symbiosis of mealybugs. Curr Biol. 2011;21:1366–1372. doi: 10.1016/j.cub.2011.06.051. [DOI] [PMC free article] [PubMed] [Google Scholar]
  272. McGowen MR, Clark C, Gatesy J. The vestigial olfactory receptor subgenome of odontocete whales: phylogenetic congruence between gene-tree reconciliation and supermatrix methods. Systatic Biol. 2008;57:574–590. doi: 10.1080/10635150802304787. [DOI] [PubMed] [Google Scholar]
  273. McGowen MR, Gatesy J, Wildman DE. Molecular evolution tracks macroevolutionary transitions in Cetacea. Trends Ecol Evol. 2014;29:336–346. doi: 10.1016/j.tree.2014.04.001. [DOI] [PubMed] [Google Scholar]
  274. McWhorter TJ, Rader JA, Schondube JE, Nicolson SW, Pinshow B, Fleming PA, Gutiérrez-Guerrero YT, Martínez del Rio C. Sucrose digestion capacity in birds shows convergent coevolution with nectar composition across continents. iScience. 2021;24:102717. doi: 10.1016/j.isci.2021.102717. [DOI] [PMC free article] [PubMed] [Google Scholar]
  275. Medeiros LP, Garcia G, Thompson JN, Guimarães PR., Jr. The geographic mosaic of coevolution in mutualistic networks. Proc Natl Acad Sci USA. 2018;115:12017–12022. doi: 10.1073/pnas.1809088115. [DOI] [PMC free article] [PubMed] [Google Scholar]
  276. Medina I, Langmore NE. Coevolution is linked with phenotypic diversification but not speciation in avian brood parasites. Proc R Soc B. 2015;282:20152056. doi: 10.1098/rspb.2015.2056. [DOI] [PMC free article] [PubMed] [Google Scholar]
  277. Megía-Palma R, Martínez J, Cuervo JJ, Belliure J, Jiménez-Robles O, Gomes V, Cabido C, Pausas JG, Fitze PS, Martín J, et al. Molecular evidence for host-parasite co-speciation between lizards and Schellackia parasites. Int J Parasitol. 2018;48:709–718. doi: 10.1016/j.ijpara.2018.03.003. [DOI] [PubMed] [Google Scholar]
  278. Merrill AE, Merriman B, Farrington-Rock C, Camacho N, Sebald E T, Funari VA, Schibler MJ, Firestein MH, Cohn ZA, Priore M A, et al. Ciliary abnormalities due to defects in the retrograde transport protein DYNC2H1 in short-rib polydactyly syndrome. Am J Hum Genet. 2009;84:542–549. doi: 10.1016/j.ajhg.2009.03.015. [DOI] [PMC free article] [PubMed] [Google Scholar]
  279. Meyer WK, Jamison J, Richter R, Woods SE, Partha R, Kowalczyk A, Kronk C, Chikina M, Bonde RK, Crocker DE, et al. Ancient convergent losses of Paraoxonase 1 yield potential risks for modern marine mammals. Science. 2018;361:591–594. doi: 10.1126/science.aap7714. [DOI] [PMC free article] [PubMed] [Google Scholar]
  280. Moeller AH, Caro-Quintero A, Mjungu D, Georgiev AV, Lonsdorf EV, Muller MN, Pusey AE, Peeters M, Hahn BH, Ochman H. Cospeciation of gut microbiota with hominids. Science. 2016;353:380–382. doi: 10.1126/science.aaf3951. [DOI] [PMC free article] [PubMed] [Google Scholar]
  281. Monge C, Leon-Velarde F. Physiological adaptation to high altitude: oxygen transport in mammals and birds. Physiol Rev. 1991;71:1135–1172. doi: 10.1152/physrev.1991.71.4.1135. [DOI] [PubMed] [Google Scholar]
  282. Monroe JG, Srikant T, Carbonell-Bejerano P, Becker C, Lensink M, Exposito-Alonso M, Klein M, Hildebrandt J, Neumann M, Kliebenstein D, et al. Mutation bias reflects natural selection in Arabidopsis thaliana. Nature. 2022;602:101–105. doi: 10.1038/s41586-021-04269-6. [DOI] [PMC free article] [PubMed] [Google Scholar]
  283. Montes N, Alonso-Blanco C, García-Arenal F. Cucumber mosaic virus infection as a potential selective pressure on Arabidopsis thaliana populations. PLoS Pathogens. 2019;15:e1007810. doi: 10.1371/journal.ppat.1007810. [DOI] [PMC free article] [PubMed] [Google Scholar]
  284. Morgan XC, Segata N, Huttenhower C. Biodiversity and functional genomics in the human microbiome. Trends Genet. 2013;29:51–58. doi: 10.1016/j.tig.2012.09.005. [DOI] [PMC free article] [PubMed] [Google Scholar]
  285. Morran LT, Schmidt OG, Gelarden IA, Parrish RC, II, Lively C M. Running with the Red Queen: host-parasite coevolution selects for biparental sex. Science. 2011;333:216–218. doi: 10.1126/science.1206360. [DOI] [PMC free article] [PubMed] [Google Scholar]
  286. Moss CF, Sinha SR. Neurobiology of echolocation in bats. Curr Opin NeuroBiol. 2003;13:751–758. doi: 10.1016/j.conb.2003.10.016. [DOI] [PubMed] [Google Scholar]
  287. Mower JP, Stefanović S, Young GJ, Palmer JD. Gene transfer from parasitic to host plants. Nature. 2004;432:165–166. doi: 10.1038/432165b. [DOI] [PubMed] [Google Scholar]
  288. Mu Y, Bian C, Liu R, Wang Y, Shao G, Li J, Qiu Y, He T, Li W, Ao J. Whole genome sequencing of a snailfish from the Yap Trench (∼7,000 m) clarifies the molecular mechanisms underlying adaptation to the deep sea. PLoS Genet. 2021;17:e1009530. doi: 10.1371/journal.pgen.1009530. [DOI] [PMC free article] [PubMed] [Google Scholar]
  289. Nachman MW, Hoekstra HE, D’Agostino SL. The genetic basis of adaptive melanism in pocket mice. Proc Natl Acad Sci USA. 2003;100:5268–5273. doi: 10.1073/pnas.0431157100. [DOI] [PMC free article] [PubMed] [Google Scholar]
  290. Naish M, Alonge M, Wlodzimierz P, Tock AJ, Abramson BW, Schmücker A, Mandáková T, Jamge B, Lambing C, Kuo P, et al. The genetic and epigenetic landscape of the Arabidopsis centromeres. Science. 2021;374:eabi7489. doi: 10.1126/science.abi7489. [DOI] [PMC free article] [PubMed] [Google Scholar]
  291. Nakamura T, Gehrke AR, Lemberg J, Szymaszek J, Shubin NH. Digits and fin rays share common developmental histories. Nature. 2016;537:225–228. doi: 10.1038/nature19322. [DOI] [PMC free article] [PubMed] [Google Scholar]
  292. Nasrallah JB. Recognition and rejection of self in plant reproduction. Science. 2002;296:305–308. doi: 10.1126/science.296.5566.305. [DOI] [PubMed] [Google Scholar]
  293. Nguyen HT, Stanton DE, Schmitz N, Farquhar GD, Ball MC. Growth responses of the mangrove Avicennia marina to salinity: development and function of shoot hydraulic systems require saline conditions. Ann Bot. 2015;115:397–407. doi: 10.1093/aob/mcu257. [DOI] [PMC free article] [PubMed] [Google Scholar]
  294. Nie Y, Speakman JR, Wu Q, Zhang C, Hu Y, Xia M, Yan L, Hambly C, Wang L, Wei W, et al. Exceptionally low daily energy expenditure in the bamboo-eating giant panda. Science. 2015;349:171–174. doi: 10.1126/science.aab2413. [DOI] [PubMed] [Google Scholar]
  295. Niu X M, Xu Y C, Li Z W, Bian Y T, Hou X H, Chen J F, Zou Y P, Jiang J, Wu Q, Ge S, et al. Transposable elements drive rapid phenotypic variation in Capsella rubella. Proc Natl Acad Sci USA. 2019;116:6908–6913. doi: 10.1073/pnas.1811498116. [DOI] [PMC free article] [PubMed] [Google Scholar]
  296. Nurk S, Koren S, Rhie A, Rautiainen M, Bzikadze AV, Mikheenko A, Vollger MR, Altemose N, Uralsky L, Gershman A, et al. The complete sequence of a human genome. Science. 2022;376:44–53. doi: 10.1126/science.abj6987. [DOI] [PMC free article] [PubMed] [Google Scholar]
  297. Olson MV. When less is more: gene loss as an engine of evolutionary change. Am J Hum Genet. 1999;64:18–23. doi: 10.1086/302219. [DOI] [PMC free article] [PubMed] [Google Scholar]
  298. Orteu A, Jiggins CD. The genomics of coloration provides insights into adaptive evolution. Nat Rev Genet. 2020;21:461–475. doi: 10.1038/s41576-020-0234-z. [DOI] [PubMed] [Google Scholar]
  299. Ortiz RM. Osmoregulation in marine mammals. J Exp Biol. 2001;204:1831–1844. doi: 10.1242/jeb.204.11.1831. [DOI] [PubMed] [Google Scholar]
  300. Ortiz RM, Worthy GAJ. Effects of capture on adrenal steroid and vasopressin concentrations in free-ranging bottlenose dolphins (Tursiops truncatus) Comp Biochem Physiol Part A. 2000;125:317–324. doi: 10.1016/S1095-6433(00)00158-6. [DOI] [PubMed] [Google Scholar]
  301. Oteiza P, Baldwin MW. Evolution of sensory systems. Curr Opin Neurobiol. 2021;71:52–59. doi: 10.1016/j.conb.2021.08.005. [DOI] [PubMed] [Google Scholar]
  302. Pan G, Xu J, Li T, Xia Q, Liu SL, Zhang G, Li S, Li C, Liu H, Yang L, et al. Comparative genomics of parasitic silkworm microsporidia reveal an association between genome expansion and host adaptation. BMC Genom. 2013;14:186. doi: 10.1186/1471-2164-14-186. [DOI] [PMC free article] [PubMed] [Google Scholar]
  303. Pan S, Lin Y, Liu Q, Duan J, Lin Z, Wang Y, Wang X, Lam SM, Zou Z, Shui G, et al. Convergent genomic signatures of flight loss in birds suggest a switch of main fuel. Nat Commun. 2019;10:2756. doi: 10.1038/s41467-019-10682-3. [DOI] [PMC free article] [PubMed] [Google Scholar]
  304. Papkou A, Guzella T, Yang W, Koepper S, Pees B, Schalkowski R, Barg MC, Rosenstiel PC, Teotónio H, Schulenburg H. The genomic basis of Red Queen dynamics during rapid reciprocal host-pathogen coevolution. Proc Natl Acad Sci USA. 2019;116:923–928. doi: 10.1073/pnas.1810402116. [DOI] [PMC free article] [PubMed] [Google Scholar]
  305. Parker J, Tsagkogeorga G, Cotton JA, Liu Y, Provero P, Stupka E, Rossiter SJ. Genome-wide signatures of convergent evolution in echolocating mammals. Nature. 2013;502:228–231. doi: 10.1038/nature12511. [DOI] [PMC free article] [PubMed] [Google Scholar]
  306. Partha R, Chauhan BK, Ferreira Z, Robinson JD, Lathrop K, Nischal KK, Chikina M, Clark NL. Subterranean mammals show convergent regression in ocular genes and enhancers, along with adaptation to tunneling. eLife. 2017;6:e25884. doi: 10.7554/eLife.25884. [DOI] [PMC free article] [PubMed] [Google Scholar]
  307. Paterson S, Vogwill T, Buckling A, Benmayor R, Spiers AJ, Thomson NR, Quail M, Smith F, Walker D, Libberton B, et al. Antagonistic coevolution accelerates molecular evolution. Nature. 2010;464:275–278. doi: 10.1038/nature08798. [DOI] [PMC free article] [PubMed] [Google Scholar]
  308. Pauly D, Pauly D, Trites A, Capuli E, Christensen V. Diet composition and trophic levels of marine mammals. ICES J Mar Sci. 1998;55:467–481. doi: 10.1006/jmsc.1997.0280. [DOI] [Google Scholar]
  309. Penfield S. Seed dormancy and germination. Curr Biol. 2017;27:R874–R878. doi: 10.1016/j.cub.2017.05.050. [DOI] [PubMed] [Google Scholar]
  310. Peng C, Ren JL, Deng C, Jiang D, Wang J, Qu J, Chang J, Yan C, Jiang K, Murphy RW, et al. The genome of Shaw’s sea snake (Hydrophis curtus) reveals secondary adaptation to its marine environment. Mol Biol Evol. 2020;37:1744–1760. doi: 10.1093/molbev/msaa043. [DOI] [PubMed] [Google Scholar]
  311. Petschenka G, Fandrich S, Sander N, Wagschal V, Boppré M, Dobler S. Stepwise evolution of resistance to toxic cardenolides via genetic substitutions in the Na+ /K+-atpase of milkweed butterflies (lepidoptera: Danaini) Evolution. 2013;67:2753–2761. doi: 10.1111/evo.12152. [DOI] [PubMed] [Google Scholar]
  312. Petschenka G, Wagschal V, von Tschirnhaus M, Donath A, Dobler S. Convergently evolved toxic secondary metabolites in plants drive the parallel molecular evolution of insect resistance. Am Natist. 2017;190:S29–S43. doi: 10.1086/691711. [DOI] [PubMed] [Google Scholar]
  313. Phillips KP, Cable J, Mohammed RS, Herdegen-Radwan M, Raubic J, Przesmycka KJ, van Oosterhout C, Radwan J. Immunogenetic novelty confers a selective advantage in host-pathogen coevolution. Proc Natl Acad Sci USA. 2018;115:1552–1557. doi: 10.1073/pnas.1708597115. [DOI] [PMC free article] [PubMed] [Google Scholar]
  314. Pichersky E, Lewinsohn E. Convergent evolution in plant specialized metabolism. Annu Rev Plant Biol. 2011;62:549–566. doi: 10.1146/annurev-arplant-042110-103814. [DOI] [PubMed] [Google Scholar]
  315. Press MO, McCoy RC, Hall AN, Akey JM, Queitsch C. Massive variation of short tandem repeats with functional consequences across strains of Arabidopsis thaliana. Genome Res. 2018;28:1169–1178. doi: 10.1101/gr.231753.117. [DOI] [PMC free article] [PubMed] [Google Scholar]
  316. Prokchorchik M, Choi S, Chung E, Won K, Dangl JL, Sohn K H. A host target of a bacterial cysteine protease virulence effector plays a key role in convergent evolution of plant innate immune system receptors. New Phytol. 2020;225:1327–1342. doi: 10.1111/nph.16218. [DOI] [PubMed] [Google Scholar]
  317. Protas ME, Patel NH. Evolution of coloration patterns. Annu Rev Cell Dev Biol. 2008;24:425–446. doi: 10.1146/annurev.cellbio.24.110707.175302. [DOI] [PubMed] [Google Scholar]
  318. Przewieslik-Allen AM, Wilkinson PA, Burridge AJ, Winfield MO, Dai X, Beaumont M, King J, Yang C, Griffiths S, Wingen LU, et al. The role of gene flow and chromosomal instability in shaping the bread wheat genome. Nat Plants. 2021;7:172–183. doi: 10.1038/s41477-020-00845-2. [DOI] [PubMed] [Google Scholar]
  319. Pyhäjärvi T, Hufford MB, Mezmouk S, Ross-Ibarra J. Complex patterns of local adaptation in teosinte. Genome Biol Evol. 2013;5:1594–1609. doi: 10.1093/gbe/evt109. [DOI] [PMC free article] [PubMed] [Google Scholar]
  320. Qin P, Lu H, Du H, Wang H, Chen W, Chen Z, He Q, Ou S, Zhang H, Li X, et al. Pan-genome analysis of 33 genetically diverse rice accessions reveals hidden genomic variations. Cell. 2021;184:3542–3558.e16. doi: 10.1016/j.cell.2021.04.046. [DOI] [PubMed] [Google Scholar]
  321. Qiu B, Larsen RS, Chang NC, Wang J, Boomsma JJ, Zhang G. Towards reconstructing the ancestral brain gene-network regulating caste differentiation in ants. Nat Ecol Evol. 2018;2:1782–1791. doi: 10.1038/s41559-018-0689-x. [DOI] [PMC free article] [PubMed] [Google Scholar]
  322. Quadrana L, Bortolini Silveira A, Mayhew GF, LeBlanc C, Martienssen RA, Jeddeloh JA, Colot V. The Arabidopsis thaliana mobilome and its impact at the species level. eLife. 2016;5:e15716. doi: 10.7554/eLife.15716. [DOI] [PMC free article] [PubMed] [Google Scholar]
  323. Regan MD, Chiang E, Liu Y, Tonelli M, Verdoorn KM, Gugel SR, Suen G, Carey HV, Assadi-Porter FM. Nitrogen recycling via gut symbionts increases in ground squirrels over the hibernation season. Science. 2022;375:460–463. doi: 10.1126/science.abh2950. [DOI] [PMC free article] [PubMed] [Google Scholar]
  324. Reimann A, Nurhayati N, Backenkohler A, Ober D. Repeated evolution of the pyrrolizidine alkaloid—mediated defense system in separate angiosperm lineages. Plant Cell. 2004;16:2772–2784. doi: 10.1105/tpc.104.023176. [DOI] [PMC free article] [PubMed] [Google Scholar]
  325. Reinar WB, Lalun VO, Reitan T, Jakobsen KS, Butenko MA. Length variation in short tandem repeats affects gene expression in natural populations of Arabidopsis thaliana. Plant Cell. 2021;33:2221–2234. doi: 10.1093/plcell/koab107. [DOI] [PMC free article] [PubMed] [Google Scholar]
  326. Ren R, Wang H, Guo C, Zhang N, Zeng L, Chen Y, Ma H, Qi J. Widespread whole genome duplications contribute to genome complexity and species diversity in angiosperms. Mol Plant. 2018;11:414–428. doi: 10.1016/j.molp.2018.01.002. [DOI] [PubMed] [Google Scholar]
  327. Rey C, Gueguen L, Semon M, Boussau B. Accurate detection of convergent amino-acid evolution with PCOC. Mol Biol Evol. 2018;35:2296–2306. doi: 10.1093/molbev/msy114. [DOI] [PMC free article] [PubMed] [Google Scholar]
  328. Rico-Guevara A, Hurme KJ, Elting R, Russell AL. Bene“fit” assessment in pollination coevolution: mechanistic perspectives on hummingbird bill-flower matching. Integrative Comp Biol. 2021;61:681–695. doi: 10.1093/icb/icab111. [DOI] [PubMed] [Google Scholar]
  329. Rokas A, Carroll SB. Frequent and widespread parallel evolution of protein sequences. Mol Biol Evol. 2008;25:1943–1953. doi: 10.1093/molbev/msn143. [DOI] [PubMed] [Google Scholar]
  330. Román-Palacios C, Wiens JJ. Recent responses to climate change reveal the drivers of species extinction and survival. Proc Natl Acad Sci USA. 2020;117:4211–4217. doi: 10.1073/pnas.1913007117. [DOI] [PMC free article] [PubMed] [Google Scholar]
  331. Romero Navarro JA, Willcox M, Burgueño J, Romay C, Swarts K, Trachsel S, Preciado E, Terron A, Delgado HV, Vidal V, et al. A study of allelic diversity underlying flowering-time adaptation in maize landraces. Nat Genet. 2017;49:476–480. doi: 10.1038/ng.3784. [DOI] [PubMed] [Google Scholar]
  332. Roscito JG, Sameith K, Parra G, Langer BE, Petzold A, Moebius C, Bickle M, Rodrigues MT, Hiller M. Phenotype loss is associated with widespread divergence of the gene regulatory landscape in evolution. Nat Commun. 2018;9:4737. doi: 10.1038/s41467-018-07122-z. [DOI] [PMC free article] [PubMed] [Google Scholar]
  333. Rosenblum EB, Parent CE, Brandt EE. The molecular basis of phenotypic convergence. Annu Rev Ecol Evol Syst. 2014;45:203–226. doi: 10.1146/annurev-ecolsys-120213-091851. [DOI] [Google Scholar]
  334. Ruan R, Guo AH, Hao YJ, Zheng JS, Wang D. De novo assembly and characterization of narrow-ridged finless porpoise renal transcriptome and identification of candidate genes involved in osmoregulation. Int J Mol Sci. 2015;16:2220–2238. doi: 10.3390/ijms16012220. [DOI] [PMC free article] [PubMed] [Google Scholar]
  335. Rudolf AM, Wu Q, Li L, Wang J, Huang Y, Togo J, Liechti C, Li M, Niu C, Nie Y, et al. A single nucleotide mutation in the dual-oxidase 2 (DUOX2) gene causes some of the panda’s unique metabolic phenotypes. Natl Sci Rev. 2022;9:nwab125. doi: 10.1093/nsr/nwab125. [DOI] [PMC free article] [PubMed] [Google Scholar]
  336. Sackton TB, Grayson P, Cloutier A, Hu Z, Liu JS, Wheeler NE, Gardner PP, Clarke JA, Baker AJ, Clamp M, et al. Convergent regulatory evolution and loss of flight in paleognathous birds. Science. 2019;364:74–78. doi: 10.1126/science.aat7244. [DOI] [PubMed] [Google Scholar]
  337. Sato JJ, Wolsan M. Loss or major reduction of umami taste sensation in pinnipeds. Naturwissenschaften. 2012;99:655–659. doi: 10.1007/s00114-012-0939-8. [DOI] [PMC free article] [PubMed] [Google Scholar]
  338. Schaller GB. Wildlife of the Tibetan Steppe. Chicago: University of Chicago Press; 1998. [Google Scholar]
  339. Schaller GB, Hu JC, Pan WS, Zhu J. The giant pandas of Wolong. Chicago: University of Chicago Press; 1986. [Google Scholar]
  340. Scheres B, van der Putten WH. The plant perceptron connects environment to development. Nature. 2017;543:337–345. doi: 10.1038/nature22010. [DOI] [PubMed] [Google Scholar]
  341. Schiestl FP, Peakall R, Mant JG, Ibarra F, Schulz C, Franke S, Francke W. The chemistry of sexual deception in an orchid-wasp pollination system. Science. 2003;302:437–438. doi: 10.1126/science.1087835. [DOI] [PubMed] [Google Scholar]
  342. Schluter D. Resource competition and coevolution in sticklebacks. Evo Edu Outreach. 2010;3:54–61. doi: 10.1007/s12052-009-0204-6. [DOI] [Google Scholar]
  343. Schneider AC, Braukmann T, Banerjee A, Stefanović S. Convergent plastome evolution and gene loss in holoparasitic lennoaceae. Genome Biol Evol. 2018;10:2663–2670. doi: 10.1093/gbe/evy190. [DOI] [PMC free article] [PubMed] [Google Scholar]
  344. Schweizer RM, Velotta JP, Ivy CM, Jones MR, Muir SM, Brad-burd GS, Storz JF, Scott GR, Cheviron ZA. Physiological and genomic evidence that selection on the transcription factor Epas1 has altered cardiovascular function in high-altitude deer mice. PLoS Genet. 2019;15:e1008420. doi: 10.1371/journal.pgen.1008420. [DOI] [PMC free article] [PubMed] [Google Scholar]
  345. Ségurel L, Thompson EE, Flutre T, Lovstad J, Venkat A, Margulis SW, Moyse J, Ross S, Gamble K, Sella G, et al. The ABO blood group is a trans-species polymorphism in primates. Proc Natl Acad Sci USA. 2012;109:18493–18498. doi: 10.1073/pnas.1210603109. [DOI] [PMC free article] [PubMed] [Google Scholar]
  346. Seidl MF, Thomma BPHJ. Transposable elements direct the coevolution between plants and microbes. Trends Genet. 2017;33:842–851. doi: 10.1016/j.tig.2017.07.003. [DOI] [PubMed] [Google Scholar]
  347. Shahid S, Kim G, Johnson NR, Wafula E, Wang F, Coruh C, Bernal-Galeano V, Phifer T, Depamphilis CW, Westwood JH, et al. MicroRNAs from the parasitic plant Cuscuta campestris target host messenger RNAs. Nature. 2018;553:82–85. doi: 10.1038/nature25027. [DOI] [PubMed] [Google Scholar]
  348. Shan H, Cheng J, Zhang R, Yao X, Kong H. Developmental mechanisms involved in the diversification of flowers. Nat Plants. 2019;5:917–923. doi: 10.1038/s41477-019-0498-5. [DOI] [PubMed] [Google Scholar]
  349. Shao Y, Li JX, Ge RL, Zhong L, Irwin DM, Murphy RW, Zhang YP. Genetic adaptations of the plateau zokor in high-elevation burrows. Sci Rep. 2015;5:17262. doi: 10.1038/srep17262. [DOI] [PMC free article] [PubMed] [Google Scholar]
  350. Sharma V, Hecker N, Roscito JG, Foerster L, Langer BE, Hiller M. A genomics approach reveals insights into the importance of gene losses for mammalian adaptations. Nat Commun. 2018;9:1215. doi: 10.1038/s41467-018-03667-1. [DOI] [PMC free article] [PubMed] [Google Scholar]
  351. Shen G, Liu N, Zhang J, Xu Y, Baldwin IT, Wu J. Cuscuta australis (dodder) parasite eavesdrops on the host plants’ FT signals to flower. Proc Natl Acad Sci USA. 2020;117:23125–23130. doi: 10.1073/pnas.2009445117. [DOI] [PMC free article] [PubMed] [Google Scholar]
  352. Shen X, De, Jonge J, Forsberg SK, Pettersson ME, Sheng Z, Hennig L, Carlborg O. Natural CMT2 variation is associated with genome-wide methylation changes and temperature seasonality. PLoS Genet. 2014;10:e1004842. doi: 10.1371/journal.pgen.1004842. [DOI] [PMC free article] [PubMed] [Google Scholar]
  353. Shindo C, Aranzana MJ, Lister C, Baxter C, Nicholls C, Nordborg M, Dean C. Role of FRIGIDA and FLOWERING LOCUS C in determining variation in flowering time of Arabidopsis. Plant Physiol. 2005;138:1163–1173. doi: 10.1104/pp.105.061309. [DOI] [PMC free article] [PubMed] [Google Scholar]
  354. Slipek NJ, Varshney J, Largaespada DA. CRISPR/Cas9-based positive screens for cancer-related traits. Methods Mol Biol. 2019;1907:137–144. doi: 10.1007/978-1-4939-8967-6_11. [DOI] [PubMed] [Google Scholar]
  355. Siefferman L, Hill GE. Structural and melanin coloration indicate parental effort and reproductive success in male eastern bluebirds. Behaval Ecol. 2003;14:855–861. doi: 10.1093/beheco/arg063. [DOI] [Google Scholar]
  356. Smith AB, Godsoe W, Rodríguez-Sánchez F, Wang HH, Warren D. Niche estimation above and below the species level. Trends Ecol Evol. 2019;34:260–273. doi: 10.1016/j.tree.2018.10.012. [DOI] [PubMed] [Google Scholar]
  357. Soberón JM. Niche and area of distribution modeling: a population ecology perspective. Ecography. 2010;33:159–167. doi: 10.1111/j.1600-0587.2009.06074.x. [DOI] [Google Scholar]
  358. Stern DL. The genetic causes of convergent evolution. Nat Rev Genet. 2013;14:751–764. doi: 10.1038/nrg3483. [DOI] [PubMed] [Google Scholar]
  359. Storey M, Jordan S. An overview of the immune system. Nurs Standard. 2008;23:47–56. doi: 10.7748/ns2008.12.23.15.47.c6738. [DOI] [PubMed] [Google Scholar]
  360. Storz JF. Causes of molecular convergence and parallelism in protein evolution. Nat Rev Genet. 2016;17:239–250. doi: 10.1038/nrg.2016.11. [DOI] [PMC free article] [PubMed] [Google Scholar]
  361. Storz JF, Cheviron ZA. Physiological genomics of adaptation to high-altitude hypoxia. Annu Rev Anim Biosci. 2021;9:149–171. doi: 10.1146/annurev-animal-072820-102736. [DOI] [PMC free article] [PubMed] [Google Scholar]
  362. Storz JF, Scott GR. Phenotypic plasticity, genetic assimilation, and genetic compensation in hypoxia adaptation of high-altitude vertebrates. Comp Biochem Physiol Part A-Mol Integr Phys. 2021;253:110865. doi: 10.1016/j.cbpa.2020.110865. [DOI] [PMC free article] [PubMed] [Google Scholar]
  363. Stuart T, Eichten SR, Cahn J, Karpievitch YV, Borevitz JO, Lister R. Population scale mapping of transposable element diversity reveals links to gene regulation and epigenomic variation. eLife. 2016;5:e20777. doi: 10.7554/eLife.20777. [DOI] [PMC free article] [PubMed] [Google Scholar]
  364. Sturm RA, Duffy DL, Box NF, Newton RA, Shepherd AG, Chen W, Marks LH, Leonard JH, Martin NG. Genetic association and cellular function of MC1R variant alleles in human pigmentation. Ann New York Acad Sci. 2003;994:348–358. doi: 10.1111/j.1749-6632.2003.tb03199.x. [DOI] [PubMed] [Google Scholar]
  365. Suetsugu K, Matsubayashi J. Evidence for mycorrhizal cheating in Apostasia nipponica, an early-diverging member of the Orchidaceae. New Phytol. 2021;229:2302–2310. doi: 10.1111/nph.17049. [DOI] [PubMed] [Google Scholar]
  366. Suetsugu K, Haraguchi TF, Tayasu I. Novel mycorrhizal cheating in a green orchid: Cremastraappendiculata depends on carbon from deadwood through fungal associations. New Phytol. 2022;235:333–343. doi: 10.1111/nph.17313. [DOI] [PubMed] [Google Scholar]
  367. Sun J, Zhang Y, Xu T, Zhang Y, Mu H, Zhang Y, Lan Y, Fields C J, Hui JHL, Zhang W, et al. Adaptation to deep-sea chemosynthetic environments as revealed by mussel genomes. Nat Ecol Evol. 2017;1:0121. doi: 10.1038/s41559-017-0121. [DOI] [PubMed] [Google Scholar]
  368. Sun L, Cao Y, Kong Q, Huang X, Yu Z, Sun D, Ren W, Yang G, Xu S. Over-expression of the bottlenose dolphin Hoxd13 gene in zebrafish provides new insights into the cetacean flipper formation. Genomics. 2021;113:2925–2933. doi: 10.1016/j.ygeno.2021.06.028. [DOI] [PubMed] [Google Scholar]
  369. Sun YB, Fu TT, Jin JQ, Murphy RW, Hillis DM, Zhang YP, Che J. Species groups distributed across elevational gradients reveal convergent and continuous genetic adaptation to high elevations. Proc Natl Acad Sci USA. 2018;115:E10634–E10641. doi: 10.1073/pnas.1813593115. [DOI] [PMC free article] [PubMed] [Google Scholar]
  370. Sureshkumar S, Todesco M, Schneeberger K, Harilal R, Balasubramanian S, Weigel D. A genetic defect caused by a triplet repeat expansion in Arabidopsis thaliana. Science. 2009;323:1060–1063. doi: 10.1126/science.1164014. [DOI] [PubMed] [Google Scholar]
  371. Teeling EC. Hear, hear: the convergent evolution of echolocation in bats? Trends Ecol Evol. 2009;24:351–354. doi: 10.1016/j.tree.2009.02.012. [DOI] [PubMed] [Google Scholar]
  372. Temeles EJ, Kress WJ. Adaptation in a plant-hummingbird association. Science. 2003;300:630–633. doi: 10.1126/science.1080003. [DOI] [PubMed] [Google Scholar]
  373. Thomas GWC, Hahn MW. Determining the null model for detecting adaptive convergence from genomic data: a case study using echolocating mammals. Mol Biol Evol. 2015;32:1232–1236. doi: 10.1093/molbev/msv013. [DOI] [PMC free article] [PubMed] [Google Scholar]
  374. Thorogood CJ, Bauer U, Hiscock SJ. Convergent and divergent evolution in carnivorous pitcher plant traps. New Phytol. 2018;217:1035–1041. doi: 10.1111/nph.14879. [DOI] [PubMed] [Google Scholar]
  375. Tkáčová J, Angelovičová M. Heat shock proteins (HSPs): a review. J Anim Sci Biotechno. 2012;45:349–353. [Google Scholar]
  376. Todesco M, Balasubramanian S, Hu TT, Traw MB, Horton M, Epple P, Kuhns C, Sureshkumar S, Schwartz C, Lanz C, et al. Natural allelic variation underlying a major fitness trade-off in Arabidopsis thaliana. Nature. 2010;465:632–636. doi: 10.1038/nature09083. [DOI] [PMC free article] [PubMed] [Google Scholar]
  377. Todesco M, Owens GL, Bercovich N, Légaré JS, Soudi S, Burge D O, Huang K, Ostevik KL, Drummond EBM, Imerovski I, et al. Massive haplotypes underlie ecotypic differentiation in sunflowers. Nature. 2020;584:602–607. doi: 10.1038/s41586-020-2467-6. [DOI] [PubMed] [Google Scholar]
  378. Tomlinson PB. The Botany of Mangroves. Cambridge: Cambridge University Press; 1986. [Google Scholar]
  379. Tong ZY, Huang SQ. The development, misuse and evidence of the concept “coevolution”. Sci Sin-Vitae. 2019;49:421–435. doi: 10.1360/N052018-00221. [DOI] [Google Scholar]
  380. Torres-Dowdall J, Karagic N, Härer A, Meyer A. Diversity in visual sensitivity across Neotropical cichlid fishes via differential expression and intraretinal variation of opsin genes. Mol Ecol. 2021;30:1880–1891. doi: 10.1111/mec.15855. [DOI] [PubMed] [Google Scholar]
  381. Tropf S, Lanz T, Rensing SA, Schröder J, Schröder G. Evidence that stilbene synthases have developed from chalcone synthases several times in the course of evolution. J Mol Evol. 1994;38:610–618. doi: 10.1007/BF00175881. [DOI] [PubMed] [Google Scholar]
  382. Valente R, Alves LQ, Nabais M, Alves F, Sousa-Pinto I, Ruivo R, Castro LFC. Convergent Cortistatin losses parallel modifications in circadian rhythmicity and energy homeostasis in Cetacea and other mammalian lineages. Genomics. 2020;113:1064–1070. doi: 10.1016/j.ygeno.2020.11.002. [DOI] [PubMed] [Google Scholar]
  383. Van Buren R, Pardo J, Man Wai C, Evans S, Bartels D. Massive tandem proliferation of elips supports convergent evolution of desiccation tolerance across land plants. Plant Physiol. 2019;179:1040–1049. doi: 10.1104/pp.18.01420. [DOI] [PMC free article] [PubMed] [Google Scholar]
  384. Van de Peer Y, Mizrachi E, Marchal K. The evolutionary significance of polyploidy. Nat Rev Genet. 2017;18:411–424. doi: 10.1038/nrg.2017.26. [DOI] [PubMed] [Google Scholar]
  385. Van Bel M, Proost S, Wischnitzki E, Movahedi S, Scheerlinck C, Van de Peer Y, Vandepoele K. Dissecting plant genomes with the PLAZA comparative genomics platform. Plant Physiol. 2012;158:590–600. doi: 10.1104/pp.111.189514. [DOI] [PMC free article] [PubMed] [Google Scholar]
  386. Vanneste K, Baele G, Maere S, Van de Peer Y. Analysis of 41 plant genomes supports a wave of successful genome duplications in association with the Cretaceous-Paleogene boundary. Genome Res. 2014;24:1334–1347. doi: 10.1101/gr.168997.113. [DOI] [PMC free article] [PubMed] [Google Scholar]
  387. Vlad D, Kierzkowski D, Rast MI, Vuolo F, Dello Ioio R, Galinha C, Gan X, Hajheidari M, Hay A, Smith RS, et al. Leaf shape evolution through duplication, regulatory diversification, and loss of a homeobox gene. Science. 2014;343:780–783. doi: 10.1126/science.1248384. [DOI] [PubMed] [Google Scholar]
  388. Vriens J, Nilius B, Voets T. Peripheral thermosensation in mammals. Nat Rev Neurosci. 2014;15:573–589. doi: 10.1038/nrn3784. [DOI] [PubMed] [Google Scholar]
  389. Waldvogel A-, Feldmeyer B, Rolshausen G, Exposito-Alonso M, Rellstab C, Kofler R, Mock T, Schmid K, Schmitt I, Bataillon T, et al. Evolutionary genomics can improve prediction of species’ responses to climate change. Evol Lett. 2020;4:4–18. doi: 10.1002/evl3.154. [DOI] [PMC free article] [PubMed] [Google Scholar]
  390. Walkowiak S, Gao L, Monat C, Haberer G, Kassa MT, Brinton J, Ramirez-Gonzalez RH, Kolodziej MC, Delorean E, Thambugala D, et al. Multiple wheat genomes reveal global variation in modern breeding. Nature. 2020;588:277–283. doi: 10.1038/s41586-020-2961-x. [DOI] [PMC free article] [PubMed] [Google Scholar]
  391. Wang G, Zhang X, Herre EA, McKey D, Machado CA, Yu WB, Cannon CH, Arnold ML, Pereira RAS, Ming R, et al. Genomic evidence of prevalent hybridization throughout the evolutionary history of the fig-wasp pollination mutualism. Nat Commun. 2021;12:718. doi: 10.1038/s41467-021-20957-3. [DOI] [PMC free article] [PubMed] [Google Scholar]
  392. Wang J, Yu X, Hu B, Zheng J, Xiao W, Hao Y, Liu W, Wang D. Physicochemical Evolution and Molecular Adaptation of the Cetacean Osmoregulation-related Gene UT-A2 and Implications for Functional Studies. Sci Rep. 2015;5:8795. doi: 10.1038/srep08795. [DOI] [PMC free article] [PubMed] [Google Scholar]
  393. Wang K, Shen Y, Yang Y, Gan X, Liu G, Hu K, Li Y, Gao Z, Zhu L, Yan G, et al. Morphology and genome of a snailfish from the Mariana Trench provide insights into deep-sea adaptation. Nat Ecol Evol. 2019;3:823–833. doi: 10.1038/s41559-019-0864-8. [DOI] [PubMed] [Google Scholar]
  394. Wang L, He L, Li J, Zhao J, Li Z, He C. Regulatory change at Physalis Organ Size 1 correlates to natural variation in tomatillo reproductive organ size. Nat Commun. 2014;5:4271. doi: 10.1038/ncomms5271. [DOI] [PubMed] [Google Scholar]
  395. Wang R, Yang Y, Jing Y, Segar ST, Zhang Y, Wang G, Chen J, Liu QF, Chen S, Chen Y, et al. Molecular mechanisms of mutualistic and antagonistic interactions in a plant-pollinator association. Nat Ecol Evol. 2021;5:974–986. doi: 10.1038/s41559-021-01469-1. [DOI] [PubMed] [Google Scholar]
  396. Wang W, Mauleon R, Hu Z, Chebotarov D, Tai S, Wu Z, Li M, Zheng T, Fuentes RR, Zhang F, et al. Genomic variation in 3,010 diverse accessions of Asian cultivated rice. Nature. 2018;557:43–49. doi: 10.1038/s41586-018-0063-9. [DOI] [PMC free article] [PubMed] [Google Scholar]
  397. Wang Y, Dai G, Gu Z, Liu G, Tang K, Pan YH, Chen Y, Lin X, Wu N, Chen H, et al. Accelerated evolution of an Lhx2 enhancer shapes mammalian social hierarchies. Cell Res. 2020;30:408–420. doi: 10.1038/s41422-020-0308-7. [DOI] [PMC free article] [PubMed] [Google Scholar]
  398. Wang Z, Xu S, Du K, Huang F, Chen Z, Zhou K, Ren W, Yang G. Evolution of digestive enzymes and RNASE1 provides insights into dietary switch of cetaceans. Mol Biol Evol. 2016;33:3144–3157. doi: 10.1093/molbev/msw191. [DOI] [PMC free article] [PubMed] [Google Scholar]
  399. Wang Z, Yuan L, Rossiter SJ, Zuo X, Ru B, Zhong H, Han N, Jones G, Jepson PD, Zhang S. Adaptive evolution of 5′ HoxD genes in the origin and diversification of the cetacean flipper. Mol Biol Evol. 2009;26:613–622. doi: 10.1093/molbev/msn282. [DOI] [PubMed] [Google Scholar]
  400. Wang Z, Ma T, Ma J, Han J, Ding L, Qiu Q. Convergent evolution of SOCS4 between yak and Tibetan antelope in response to high-altitude stress. Gene. 2015;572:298–302. doi: 10.1016/j.gene.2015.08.024. [DOI] [PubMed] [Google Scholar]
  401. Weber JM. The physiology of long-distance migration: extending the limits of endurance metabolism. J Exp Biol. 2009;212:593–597. doi: 10.1242/jeb.015024. [DOI] [PubMed] [Google Scholar]
  402. Week B, Nuismer SL. The measurement of coevolution in the wild. Ecol Lett. 2019;22:717–725. doi: 10.1111/ele.13231. [DOI] [PubMed] [Google Scholar]
  403. Wei DB, Ma JB. Comparison of the content of myoglobin and lactate dehydrogenase in cardiac and skeleton muscle of plateau zorkor and mouse. J Qinghai Univ. 2001;19:20–21. [Google Scholar]
  404. Wei DB, Wei L, Zhang JM, Yu HY. Blood-gas properties of plateau zokor (Myospalax baileyi) Comp Biochem Phys Part A-Mol Integr Phys. 2006;145:372–375. doi: 10.1016/j.cbpa.2006.07.011. [DOI] [PubMed] [Google Scholar]
  405. Wei FW. A new era for evolutionary developmental biology in non-model organisms. Sci China Life Sci. 2020;63:1251–1253. doi: 10.1007/s11427-020-1748-0. [DOI] [PubMed] [Google Scholar]
  406. Wei L, Cao X. The effect of transposable elements on phenotypic variation: insights from plants to humans. Sci China Life Sci. 2016;59:24–37. doi: 10.1007/s11427-015-4993-2. [DOI] [PubMed] [Google Scholar]
  407. Weiblen GD. How to be a fig wasp. Annu Rev Entomol. 2002;47:299–330. doi: 10.1146/annurev.ento.47.091201.145213. [DOI] [PubMed] [Google Scholar]
  408. Weigel D. Natural variation in Arabidopsis: from molecular genetics to ecological genomics. Plant Physiol. 2012;158:2–22. doi: 10.1104/pp.111.189845. [DOI] [PMC free article] [PubMed] [Google Scholar]
  409. Wells JN, Feschotte C. A field guide to eukaryotic transposable elements. Annu Rev Genet. 2020;54:539–561. doi: 10.1146/annurev-genet-040620-022145. [DOI] [PMC free article] [PubMed] [Google Scholar]
  410. Wilson AM, Hubel TY, Wilshin SD, Lowe JC, Lorenc M, Dewhirst OP, Bartlam-Brooks HLA, Diack R, Bennitt E, Golabek KA, et al. Biomechanics of predator-prey arms race in lion, zebra, cheetah and impala. Nature. 2018;554:183–188. doi: 10.1038/nature25479. [DOI] [PubMed] [Google Scholar]
  411. Wu Q, Wang X, Ding Y, Hu Y, Nie Y, Wei W, Ma S, Yan L, Zhu L, Wei F. Seasonal variation in nutrient utilization shapes gut microbiome structure and function in wild giant pandas. Proc R Soc B. 2017;284:20170955. doi: 10.1098/rspb.2017.0955. [DOI] [PMC free article] [PubMed] [Google Scholar]
  412. Wu C, Zhang D, Kan M, Lv Z, Zhu A, Su Y, Zhou D, Zhang J, Zhang Z, Xu M, et al. The draft genome of the large yellow croaker reveals well-developed innate immunity. Nat Commun. 2014;5:5227. doi: 10.1038/ncomms6227. [DOI] [PMC free article] [PubMed] [Google Scholar]
  413. Wu HJ, Zhang Z, Wang JY, Oh DH, Dassanayake M, Liu B, Huang Q, Sun HX, Xia R, Wu Y, et al. Insights into salt tolerance from the genome of Thellungiella salsuginea. Proc Natl Acad Sci USA. 2012;109:12219–12224. doi: 10.1073/pnas.1209954109. [DOI] [PMC free article] [PubMed] [Google Scholar]
  414. Wu P, Jiang TX, Suksaweang S, Widelitz RB, Chuong CM. Molecular shaping of the beak. Science. 2004;305:1465–1466. doi: 10.1126/science.1098109. [DOI] [PMC free article] [PubMed] [Google Scholar]
  415. Wu Q, Han T S, Chen X, Chen J F, Zou Y P, Li Z W, Xu Y C, Guo YL. Long-term balancing selection contributes to adaptation in Arabidopsis and its relatives. Genome Biol. 2017;18:217. doi: 10.1186/s13059-017-1342-8. [DOI] [PMC free article] [PubMed] [Google Scholar]
  416. Wu S, Han B, Jiao Y. Genetic contribution of paleopolyploidy to adaptive evolution in angiosperms. Mol Plant. 2019;13:59–71. doi: 10.1016/j.molp.2019.10.012. [DOI] [PubMed] [Google Scholar]
  417. Wu T, Kayser B. High altitude adaptation in Tibetans. High Altitude Med Biol. 2006;7:193–208. doi: 10.1089/ham.2006.7.193. [DOI] [PubMed] [Google Scholar]
  418. Wu W, Liu X, Wang M, Meyer RS, Luo X, Ndjiondjop MN, Tan L, Zhang J, Wu J, Cai H, et al. A single-nucleotide polymorphism causes smaller grain size and loss of seed shattering during African rice domestication. Nat Plants. 2017;3:17064. doi: 10.1038/nplants.2017.64. [DOI] [PubMed] [Google Scholar]
  419. Wu Y, Lin F, Zhou Y, Wang J, Sun S, Wang B, Zhang Z, Li G, Lin X, Wang X, et al. Genomic mosaicism due to homoeologous exchange generates extensive phenotypic diversity in nascent allopolyploids. Natl Sci Rev. 2021;8:nwaa277. doi: 10.1093/nsr/nwaa277. [DOI] [PMC free article] [PubMed] [Google Scholar]
  420. Xi Z, Wang Y, Bradley R K, Sugumaran M, Marx C J, Rest J S, Davis C C. Massive mitochondrial gene transfer in a parasitic flowering plant clade. PLoS Genet. 2013;9:e1003265. doi: 10.1371/journal.pgen.1003265. [DOI] [PMC free article] [PubMed] [Google Scholar]
  421. Xia J, Guo Z, Yang Z, Han H, Wang S, Xu H, Yang X, Yang F, Wu Q, Xie W, et al. Whitefly hijacks a plant detoxification gene that neutralizes plant toxins. Cell. 2021;184:1693–1705.e17. doi: 10.1016/j.cell.2021.02.014. [DOI] [PubMed] [Google Scholar]
  422. Xiong Z, Gaeta RT, Pires JC. Homoeologous shuffling and chromosome compensation maintain genome balance in resynthesized allopolyploid Brassica napus. Proc Natl Acad Sci USA. 2011;108:7908–7913. doi: 10.1073/pnas.1014138108. [DOI] [PMC free article] [PubMed] [Google Scholar]
  423. Xu D, Yang C, Shen Q, Pan S, Liu Z, Zhang T, Zhou X, Lei M, Chen P, Yang H, et al. A single mutation underlying phenotypic convergence for hypoxia adaptation on the Qinghai-Tibetan Plateau. Cell Res. 2021;31:1032–1035. doi: 10.1038/s41422-021-00517-6. [DOI] [PMC free article] [PubMed] [Google Scholar]
  424. Xu, S., Guo, Z., Feng, X., Shao, S., Yang, Y., Li, J., Zhong, C., He, Z., and Shi, S. (2021b). Where whole-genome duplication is most beneficial: Adaptation of mangroves to a wide salinity range between land and sea. Mol Ecol, doi: 10.1111/mec.16320. [DOI] [PubMed]
  425. Xu, S., He, Z., Guo, Z., Zhang, Z., Wyckoff, G.J., Greenberg, A., Wu, C.I., and Shi, S. (2017). Genome-wide convergence during evolution of mangroves from woody plants. Mol Biol Evol msw277. [DOI] [PubMed]
  426. Xu S, Wang J, Guo Z, He Z, Shi S. Genomic convergence in the adaptation to extreme environments. Plant Commun. 2020;1:100117. doi: 10.1016/j.xplc.2020.100117. [DOI] [PMC free article] [PubMed] [Google Scholar]
  427. Xu S, Yang Y, Zhou X, Xu J, Zhou K, Yang G. Adaptive evolution of the osmoregulation-related genes in cetaceans during secondary aquatic adaptation. BMC Evol Biol. 2013;13:1–9. doi: 10.1186/1471-2148-13-189. [DOI] [PMC free article] [PubMed] [Google Scholar]
  428. Xu X, Liu X, Ge S, Jensen JD, Hu F, Li X, Dong Y, Gutenkunst RN, Fang L, Huang L, et al. Resequencing 50 accessions of cultivated and wild rice yields markers for identifying agronomically important genes. Nat Biotechnol. 2012;30:105–111. doi: 10.1038/nbt.2050. [DOI] [PubMed] [Google Scholar]
  429. Xu YC, Niu XM, Li XX, He W, Chen JF, Zou YP, Wu Q, Zhang YE, Busch W, Guo YL. Adaptation and phenotypic diversification in Arabidopsis through loss-of-function mutations in protein-coding genes. Plant Cell. 2019;31:1012–1025. doi: 10.1105/tpc.18.00791. [DOI] [PMC free article] [PubMed] [Google Scholar]
  430. Yancey PH. Cellular responses in marine animals to hydrostatic pressure. J Exp Zool 3 3. 2020;3:398–420. doi: 10.1002/jez.2354. [DOI] [PubMed] [Google Scholar]
  431. Yang H, Lyu B, Yin HQ, Li SQ. Comparative transcriptomics highlights convergent evolution of energy metabolic pathways in group-living spiders. Zool Res. 2021;42:195–206. doi: 10.24272/j.issn.2095-8137.2020.281. [DOI] [PMC free article] [PubMed] [Google Scholar]
  432. Yang H, Yang S, Fan F, Li Y, Dai S, Zhou X, Steiner CC, Coppedge B, Roos C, Cai X, et al. A new world monkey resembles human in bitter taste receptor evolution and function via a single parallel amino acid substitution. Mol Biol Evol. 2021;38:5472–479. doi: 10.1093/molbev/msab263. [DOI] [PMC free article] [PubMed] [Google Scholar]
  433. Yang J, Chen X, Bai J, Fang D, Qiu Y, Jiang W, Yuan H, Bian C, Lu J, He S, et al. The Sinocyclocheilus cavefish genome provides insights into cave adaptation. BMC Biol. 2016;14:1–3. doi: 10.1186/s12915-015-0223-4. [DOI] [PMC free article] [PubMed] [Google Scholar]
  434. Yang L, Wang R. Asymmetric interactions in fig-fig wasp mutualism. Biodiv Sci. 2020;28:1324–1332. doi: 10.17520/biods.2020234. [DOI] [Google Scholar]
  435. Yang L, Wang HN, Hou XH, Zou YP, Han TS, Niu XM, Zhang J, Zhao Z, Todesco M, Balasubramanian S, et al. Parallel evolution of common allelic variants confers flowering diversity in Capsella rubella. Plant Cell. 2018;30:1322–1336. doi: 10.1105/tpc.18.00124. [DOI] [PMC free article] [PubMed] [Google Scholar]
  436. Yang S, Lu X, Wang Y, Xu L, Chen X, Yang F, Lai R. A paradigm of thermal adaptation in penguins and elephants by tuning cold activation in TRPM8. Proc Natl Acad Sci USA. 2020;117:8633–8638. doi: 10.1073/pnas.1922714117. [DOI] [PMC free article] [PubMed] [Google Scholar]
  437. Yang X, Hu R, Yin H, Jenkins J, Shu S, Tang H, Liu D, Weighill DA, Cheol Yim W, Ha J, et al. The Kalanchoë genome provides insights into convergent evolution and building blocks of crassulacean acid metabolism. Nat Commun. 2017;8:1899. doi: 10.1038/s41467-017-01491-7. [DOI] [PMC free article] [PubMed] [Google Scholar]
  438. Yang X, Pang HB, Liu BL, Qiu ZJ, Gao Q, Wei L, Dong Y, Wang YZ. Evolution of double positive autoregulatory feedback loops in CYCLOIDEA2 clade genes is associated with the origin of floral zygomorphy. Plant Cell. 2012;24:1834–1847. doi: 10.1105/tpc.112.099457. [DOI] [PMC free article] [PubMed] [Google Scholar]
  439. Yang Z, Wafula EK, Kim G, Shahid S, McNeal JR, Ralph PE, Timilsena PR, Yu W, Kelly EA, Zhang H, et al. Convergent horizontal gene transfer and cross-talk of mobile nucleic acids in parasitic plants. Nat Plants. 2019;5:991–1001. doi: 10.1038/s41477-019-0458-0. [DOI] [PubMed] [Google Scholar]
  440. Yeaman S, Hodgins KA, Lotterhos KE, Suren H, Nadeau S, Degner JC, Nurkowski KA, Smets P, Wang T, Gray LK, et al. Convergent local adaptation to climate in distantly related conifers. Science. 2016;353:1431–1433. doi: 10.1126/science.aaf7812. [DOI] [PubMed] [Google Scholar]
  441. Yin D, Zhou R, Yin M, Chen Y, Xu S, Yang G. Gene duplication and loss of AANAT in mammals driven by rhythmic adaptations. Mol Biol Evol. 2021;38:3925–3937. doi: 10.1093/molbev/msab125. [DOI] [PMC free article] [PubMed] [Google Scholar]
  442. Yoshida T, Jones LE, Ellner SP, Fussmann GF, Hairston NG., Jr Rapid evolution drives ecological dynamics in a predator-prey system. Nature. 2003;424:303–306. doi: 10.1038/nature01767. [DOI] [PubMed] [Google Scholar]
  443. Youngblut ND, Reischer GH, Walters W, Schuster N, Walzer C, Stalder G, Ley RE, Farnleitner AH. Host diet and evolutionary history explain different aspects of gut microbiome diversity among vertebrate clades. Nat Commun. 2019;10:2200. doi: 10.1038/s41467-019-10191-3. [DOI] [PMC free article] [PubMed] [Google Scholar]
  444. Yu C, Yan C, Liu Y, Liu Y, Jia Y, Lavelle D, An G, Zhang W, Zhang L, Han R, et al. Upregulation of a KN1 homolog by transposon insertion promotes leafy head development in lettuce. Proc Natl Acad Sci USA. 2020;117:33668–33678. doi: 10.1073/pnas.2019698117. [DOI] [PMC free article] [PubMed] [Google Scholar]
  445. Yu L, Wang GD, Ruan J, Chen YB, Yang CP, Cao X, Wu H, Liu YH, Du ZL, Wang XP, et al. Genomic analysis of snubnosed monkeys (Rhinopithecus) identifies genes and processes related to high-altitude adaptation. Nat Genet. 2016;48:947–952. doi: 10.1038/ng.3615. [DOI] [PubMed] [Google Scholar]
  446. Yuan Y, Zhang Y, Zhang P, Liu C, Wang J, Gao H, Hoelzel AR, Seim I, Lv M, Lin M, et al. Comparative genomics provides insights into the aquatic adaptations of mammals. Proc Natl Acad Sci USA. 2021;118:e2106080118. doi: 10.1073/pnas.2106080118. [DOI] [PMC free article] [PubMed] [Google Scholar]
  447. Yusuf L, Heatley MC, Palmer JPG, Barton HJ, Cooney CR, Gossmann TI. Noncoding regions underpin avian bill shape diversification at macroevolutionary scales. Genome Res. 2020;30:553–565. doi: 10.1101/gr.255752.119. [DOI] [PMC free article] [PubMed] [Google Scholar]
  448. Zeng J, Wang Z, Shi Z. Metabolic characteristics and some physiological parameters of mole rat (Myospalax baileyi) in alpine area. Acta Biol Plat Sin. 1984;3:163–171. [Google Scholar]
  449. Zhang D, Zhang Z, Unver T, Zhang B. CRISPR/Cas: a powerful tool for gene function study and crop improvement. J Adv Res. 2021;29:207–221. doi: 10.1016/j.jare.2020.10.003. [DOI] [PMC free article] [PubMed] [Google Scholar]
  450. Zhang H, Bian Y, Gou X, Dong Y, Rustgi S, Zhang B, Xu C, Li N, Qi B, Han F, et al. Intrinsic karyotype stability and gene copy number variations may have laid the foundation for tetraploid wheat formation. Proc Natl Acad Sci USA. 2013;110:19466–19471. doi: 10.1073/pnas.1319598110. [DOI] [PMC free article] [PubMed] [Google Scholar]
  451. Zhang H, Zhu J, Gong Z, Zhu JK. Abiotic stress responses in plants. Nat Rev Genet. 2022;23:104–119. doi: 10.1038/s41576-021-00413-0. [DOI] [PubMed] [Google Scholar]
  452. Zhang J, Kumar S. Detection of convergent and parallel evolution at the amino acid sequence level. Mol Biol Evol. 1997;14:527–536. doi: 10.1093/oxfordjournals.molbev.a025789. [DOI] [PubMed] [Google Scholar]
  453. Zhang L, Hu J, Han X, Li J, Gao Y, Richards CM, Zhang C, Tian Y, Liu G, Gul H, et al. A high-quality apple genome assembly reveals the association of a retrotransposon and red fruit colour. Nat Commun. 2019;10:1494. doi: 10.1038/s41467-019-09518-x. [DOI] [PMC free article] [PubMed] [Google Scholar]
  454. Zhang L, Wu S, Chang X, Wang X, Zhao Y, Xia Y, Trigiano RN, Jiao Y, Chen F. The ancient wave of polyploidization events in flowering plants and their facilitated adaptation to environmental stress. Plant Cell Environ. 2020;43:2847–2856. doi: 10.1111/pce.13898. [DOI] [PubMed] [Google Scholar]
  455. Zhang T, Chen J, Zhang J, Guo Y-T, Zhou X, Li M-W, Zheng Z-Z, Zhang T-Z, Murphy RW, Nevo E, et al. Phenotypic and genomic adaptations to the extremely high elevation in plateau zokor (Myospalax baileyi) Mol Ecol. 2021;30:5765–5779. doi: 10.1111/mec.16174. [DOI] [PubMed] [Google Scholar]
  456. Zhang W, Liu J, Zhang Y, Qiu J, Li Y, Zheng B, Hu F, Dai S, Huang X. A high-quality genome sequence of alkaligrass provides insights into halophyte stress tolerance. Sci China Life Sci. 2020;63:1269–1282. doi: 10.1007/s11427-020-1662-x. [DOI] [PubMed] [Google Scholar]
  457. Zhang X, Wang G, Zhang S, Chen S, Wang Y, Wen P, Ma X, Shi Y, Qi R, Yang Y, et al. Genomes of the Banyan tree and pollinator wasp provide insights into fig-wasp coevolution. Cell. 2020;183:875–889.e17. doi: 10.1016/j.cell.2020.09.043. [DOI] [PubMed] [Google Scholar]
  458. Zhang Y, Li G. Advances in technologies for 3D genomics research. Sci China Life Sci. 2020;63:811–824. doi: 10.1007/s11427-019-1704-2. [DOI] [PubMed] [Google Scholar]
  459. Zhang Z, Qu C, Yao R, Nie Y, Xu C, Miao J, Zhong B. The parallel molecular adaptations to the Antarctic cold environment in two psychrophilic green algae. Genome Biol Evol. 2019;11:1897–1908. doi: 10.1093/gbe/evz104. [DOI] [PMC free article] [PubMed] [Google Scholar]
  460. Zhang Z, Xu D, Wang L, Hao J, Wang J, Zhou X, Wang W, Qiu Q, Huang X, Zhou J, et al. Convergent evolution of rumen microbiomes in high-altitude mammals. Curr Biol. 2016;26:1873–1879. doi: 10.1016/j.cub.2016.05.012. [DOI] [PubMed] [Google Scholar]
  461. Zhao YP, Fan G, Yin PP, Sun S, Li N, Hong X, Hu G, Zhang H, Zhang FM, Han JD, et al. Resequencing 545 ginkgo genomes across the world reveals the evolutionary history of the living fossil. Nat Commun. 2019;10:4201. doi: 10.1038/s41467-019-12133-5. [DOI] [PMC free article] [PubMed] [Google Scholar]
  462. Zhdanova IV, Lynch HJ, Wurtman RJ. Melatonin: a sleep-promoting hormone. Sleep. 1997;20:899–907. [PubMed] [Google Scholar]
  463. Zhen Y, Aardema ML, Medina EM, Schumer M, Andolfatto P. Parallel molecular evolution in an herbivore community. Science. 2012;337:1634–1637. doi: 10.1126/science.1226630. [DOI] [PMC free article] [PubMed] [Google Scholar]
  464. Zheng Z, Hua R, Xu G, Yang H, Shi P. Gene losses may contribute to subterranean adaptations in naked mole-rat and blind mole-rat. BMC Biol. 2022;20:44. doi: 10.1186/s12915-022-01243-0. [DOI] [PMC free article] [PubMed] [Google Scholar]
  465. Zhong S, Liu M, Wang Z, Huang Q, Hou S, Xu YC, Ge Z, Song Z, Huang J, Qiu X, et al. Cysteine-rich peptides promote interspecific genetic isolation in Arabidopsis. Science. 2019;364:9564. doi: 10.1126/science.aau9564. [DOI] [PMC free article] [PubMed] [Google Scholar]
  466. Zhou W, Yang S, Li B, Nie Y, Luo A, Huang G, Liu X, Lai R, Wei F. Why wild giant pandas frequently roll in horse manure. Proc Natl Acad Sci USA. 2020;117:32493–32498. doi: 10.1073/pnas.2004640117. [DOI] [PMC free article] [PubMed] [Google Scholar]
  467. Zhou X, Guang X, Sun D, Xu S, Li M, Seim I, Jie W, Yang L, Zhu Q, Xu J, et al. Population genomics of finless porpoises reveal an incipient cetacean species adapted to freshwater. Nat Commun. 2018;9:1276. doi: 10.1038/s41467-018-03722-x. [DOI] [PMC free article] [PubMed] [Google Scholar]
  468. Zhou X, Seim I, Gladyshev VN. Convergent evolution of marine mammals is associated with distinct substitutions in common genes. Sci Rep. 2015;5:16550. doi: 10.1038/srep16550. [DOI] [PMC free article] [PubMed] [Google Scholar]
  469. Zhou Y, Zhao X, Li Y, Xu J, Bi A, Kang L, Xu D, Chen H, Wang Y, Wang Y, et al. Triticum population sequencing provides insights into wheat adaptation. Nat Genet. 2020;52:1412–1422. doi: 10.1038/s41588-020-00722-w. [DOI] [PubMed] [Google Scholar]
  470. Zhu K, Zhou X, Xu S, Sun D, Ren W, Zhou K, Yang G. The loss of taste genes in cetaceans. BMC Evol Biol. 2014;14:218. doi: 10.1186/s12862-014-0218-8. [DOI] [PMC free article] [PubMed] [Google Scholar]
  471. Zhu L, Wu Q, Dai J, Zhang S, Wei F. Evidence of cellulose metabolism by the giant panda gut microbiome. Proc Natl Acad Sci USA. 2011;108:17714–17719. doi: 10.1073/pnas.1017956108. [DOI] [PMC free article] [PubMed] [Google Scholar]
  472. Zhu X, Guan Y, Signore AV, Natarajan C, DuBay SG, Cheng Y, Han N, Song G, Qu Y, Moriyama H, et al. Divergent and parallel routes of biochemical adaptation in high-altitude passerine birds from the Qinghai-Tibet Plateau. Proc Natl Acad Sci USA. 2018;115:1865–1870. doi: 10.1073/pnas.1720487115. [DOI] [PMC free article] [PubMed] [Google Scholar]
  473. Zou YP, Hou XH, Wu Q, Chen JF, Li ZW, Han TS, Niu XM, Yang L, Xu YC, Zhang J, et al. Adaptation of Arabidopsis thaliana to the Yangtze River basin. Genome Biol. 2017;18:239. doi: 10.1186/s13059-017-1378-9. [DOI] [PMC free article] [PubMed] [Google Scholar]
  474. Zou Z, Zhang J. No genome-wide protein sequence convergence for echolocation. Mol Biol Evol. 2015;32:1237–1241. doi: 10.1093/molbev/msv014. [DOI] [PMC free article] [PubMed] [Google Scholar]
  475. Zou Z, Zhang J. Are convergent and parallel amino acid substitutions in protein evolution more prevalent than neutral expectations? Mol Biol Evol. 2015;32:2085–2096. doi: 10.1093/molbev/msv091. [DOI] [PMC free article] [PubMed] [Google Scholar]
  476. Zou Z, Zhang J. Gene tree discordance does not explain away the temporal decline of convergence in mammalian protein sequence evolution. Mol Biol Evol. 2017;34:1682–1688. doi: 10.1093/molbev/msx109. [DOI] [PMC free article] [PubMed] [Google Scholar]

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