PUBLICATIONS

*corresponding author; †equal contribution.

62. Lu S, Fang C, Zeng H, Hu R, Wei C, Miao R, Gan X, Guo B*, Yao M*, He S*. (2026) Advancing biological taxonomy in the AI era: deep learning applications, challenges, and future directions. Science China Life Sciences, doi:10.1007/s11427-025-3074-8, in press. [link][PopSci in Chinese]

61. Tu W, Li Y, Du Y, Ding J, Zhang Q, Xi Y, Wang Y, Han L, Qi T, Zhao Z, Dai Y, Shi M, Gu S, Guo Baocheng*, Liu X*. (2026) Invasive predator reshapes island trophic network and biogeography. Current Biology, doi:10.1016/j.cub.2025.11.017, in press. [link]

60. Xu S, Zhao Y*, Zhao Y, Wang C, Li X, Guo B*. (2026) Different growth patterns in cave-adapted Sinocyclocheilus fish species. Environmental Biology of Fishes, 109:3. [link]

59. Xu S†, Zhang M†, Meng F, Wang C, Li X*, Guo B*. (2025) Convergent subgenome dominance but with lineage-specific functional divergence of homoeologs during cave adaptation: Insights from full-length transcriptomes of Sinocyclocheilus species. Frontiers in Zoology, doi:10.1186/s12983-025-00591-1, in press. [link]

58. Montero-Mendieta S†, Wang Y†, Wang C, Meng F, Zhao Y, Li X*, Guo B*. (2025) Doubled genomes, divergent fates: Genomic insights into diversification in an allotetraploid cavefish. Molecular Ecology, 34:e70118. [link]

57. Rozimov A, Turaev L, Namozov S, Agzamov F, Sobirov J, Wang C, Kholmatov B, Li X*, Guo B. (2025) Implications for habitat suitability using length-weight relationships and condition factors in the Chirchik River, Syr Darya Basin. Journal of Applied Ichthyology, 2025:6648940. [link]

56. Zhang M†, Zhao Q†, Huang J†, Zou M, Guo B*, Zhao Y*, Meng F*. (2025) A splicing mutation in mitfa is involved in the depigmentation of cavefish Triplophysa rosa. Molecular Biology and Evolution, 42:msaf175. [link]

Selected as cover story. [link]

55. Ding Y, Zou M, Guo B*. (2025) Genomic signatures associated with recurrent scale loss in cyprinid fish. Integrative Zoology, 20:535-550. [link]

54. Luo M†, Zhao J†, Merilä J, Barrett RDH, Guo B*, Hu J*. (2025) The interplay between epigenomic and transcriptomic variation during ecotype divergence in stickleback. BMC Biology, 23:70. [link]

53. Liu Z†, Wang C†, Guo B*. (2025) Biodiversity – the cornerstone of sustainable aquaculture development: Insights from the breeding of approved fish varieties for aquaculture from 1996 to 2024 in China. Reviews in Aquaculture, 17:e70003. [link][PopSci in Chinese]

52. Rozimov A†, Wang Yufan†, Wang M, Zou M, Sobirov J, Karimov E, Kholmatov B, Freyhof J, Namozov S, Wang C, Li X*, Guo B. (2025) Mitochondrial genome insights into the phylogenetics, taxonomy, and biogeographic evolution of snow trout (Cyprinidae: Schizothorax) in the Tien Shan mountains. Zoosystematics and Evolution, 101:91-102. [link]

51. Cheng R, Luo A, Orr M, Ge D, Hou Ze, Qu Y, Guo B, Zhang F, Sha Z, Zhao Z, Wang M, Shi, Han H, Zhou Q, Li Y, Liu X, Shao C, Zhang A, Zhou Z, Zhu C*. (2025) Cryptic diversity begets challenges and opportunities in biodiversity research. Integrative Zoology, 20:33-49. [link]

50. Li X, Guan X, Liu Z, Wang Yingnan, Wang C, Montero-Mendieta S, Zhao Y, Pan G, Tolebek B, Qu H, Lan W, Guo B*. (2024) Discovery of a new distribution site for the Crucian Carp (Carassius carassius), a first-class protected wild animal of the Xinjiang Uygur Autonomous Region, in the Irtysh River basin. Chinese Journal of Zoology, 59:990-992. (in Chinese) [link]

49. Tu W, Du Y, Stuart YE, Li Y, Wang Y, Wu Q, Guo B*, Liu X*. (2024) Biological invasion is eroding the unique assembly of island herpetofauna worldwide. Biological Conservation, 300:110853. [link]

48. Li X, Wang M, Zou M, Guan X, Xu S, Chen W, Wang C, Chen Y*, He S*, Guo B*. (2024) Recent and recurrent autopolyploidization fueled diversification of snow carp on the Tibetan Plateau. Molecular Biology and Evolution, 41:msae221. [link] [PopSci in Chinese]

47. Zhang T†, Tan S†, Tang N†, Li Y†, Zhang C, Sun J, Guo Y, Gao H, Cai Y, Sun W, Wang C, Fu L, Ma H, Wu Y, Hu X, Zhang X, Gee P, Yan W, Zhao Y, Chen Q, Guo B, Wang H*, Zhang YE*. (2024) Heterologous survey of 130 DNA transposons in human cells highlights their functional divergence and expands the genome engineering toolbox. Cell, 187:3741-3760. [link]

46. Du Y†, Xi Y†, Yang Z†, Gu D†, Zhang Z†, Tu W, Zeng Y, Cui R, Yan Z, Xin Y, Jin W, Zhang Y, Yang L, Guo B, Ke Z, Rohr JR, Liu X*. (2024) High risk of biological invasion from prayer animal release in China. Frontiers in Ecology and the Environment, 22: e2647. [link]

45. Wang M†, Li X†, Wang C, Zou M, Yang J, Li XD, Guo B*. (2024) Asymmetric and parallel subgenome selection co-shape common carp domestication. BMC Biology, 22:4. [link]

44. Du Y†, Tu W†, Yang L, Gu D, Guo B*, Liu X*. (2023) Review of the impacts of invasive alien vertebrates on biodiversity. Scientia Sinica Vitae, 53:1035-1054. (in Chinese) [link]

43. Yang L†, Sun N†, Zeng H†, Wang Y†, Chen W, Ding Z, Liu Y, Wang J, Meng M, Shen Y, Kang J, Ma X, Lv W, Chen J, Meyer A*, Guo B*, He S*. (2023) Enlarged fins of Tibetan catfish provide new evidence of adaptation to high plateau. Science China Life Sciences, 66:1554-1568. [link]

42. Wang Yu, Wang Yingnan, Cheng X, Ding Y, Wang C, Merilä J, Guo B*. (2023) Prevalent introgression underlies convergent evolution in the diversification of Pungitius sticklebacks. Molecular Biology and Evolution, 40:msad026. [link]

41. Xie W†, Wen Z†, Song K, Guo B*, Fang Y, Sun Y*. (2023) A global freshwater assessment of establishment risk for the invasive Alligator Gar (Atractosteus spatula), and the risks to freshwater ecosystems in China. Zoological Research, 44:90-93. [link]

40. Wang Yingnan, Wang Yu, Zhao Y, Kravchenko A, Merilä J, Guo B*. (2022) Phylogenomics of Northeast Asian Pungitius sticklebacks. Diversity and Distributions, 28:2610–2621. [link]

39. Ge D*, Qu Y*, Deng T, Thuiller W, Fišer C, Ericson PGP, Guo B, de la Sancha NU, von der Heyden S, Hou Z, Li J, Abramov A, Vogler AP, Jønsson KA, Mittermeier R. (2022) New progress in exploring the mechanisms underlying extraordinarily high biodiversity in global hotspots and their implications for conservation. Diversity and Distributions, 28:2448-2458. [link]

38. Wang Yingnan & Guo B*. (2022) Distribution status of Pungitius sticklebacks in China. Chinese Journal of Zoology, 57:787-798. (in Chinese) [link] [PopSci in Chinese]

37. Jin L, Li Z, Wang C, Wang Yingnan, Li X, Yang J, Zhao Y, Guo B*. (2022) Contrasting population differentiation in two sympatric Triplophysa loaches on the Qinghai-Tibet Plateau. Frontiers in Genetics, 13:958076. [link] [PopSci in Chinese]

36. Guo B*, Zou M, Sakamoto T, Innan H*. (2022) Functional innovation through gene duplication followed by frameshift mutation. Genes, 13:190. [link]

35. Jin L & Guo B*. (2021). Detecting adaptive loci with population genomic data. Bio-101: e1010627. Doi: 10.21769/BioProtoc.1010627. (in Chinese) [link]

34. Jin L & Guo B*. (2021). Detecting loci underlying local adaptation using environmental association analysis. Bio-101: e1010615. Doi: 10.21769/BioProtoc.1010615. (in Chinese) [link]

33. Wang Yuwei & Guo B*. (2021) The divergence of alternative splicing between ohnologs in teleost fishes. BMC Ecology and Evolution, 21:98. [link]

32. Kemppainen P*, Li Z, Rastas P, Löytynoja A, Fang B, Yang J, Guo B, Shikano T, Merilä J. (2021) Genetic population structure constrains local adaptation in sticklebacks. Molecular Ecology, 30:1946–1961. [link]

Selected as cover story. [link]

Commentary by Yamasaki & Kitano. (2021) Multiple paths to the same destination: influence of gene flow on convergent evolution. Molecular Ecology, 30:1939–1942. [link]

Preprint: bioRxiv, 2020.01.17.908970. [link]

31. Wang Yingnan, Zhao Y, Wang Yu, Li Z, Guo B*, Merilä J. (2020) Population transcriptomics reveals weak parallel genetic basis in repeated marine and freshwater divergence in nine-spined sticklebacks. Molecular Ecology, 29:1642-1656. [link]

30. Yang T, Meng W*, Guo B*. (2020) Population genomic analysis of two endemic schizothoracins reveals their genetic differences and adaptation to altitude and temperature. Animals, 10: 447. [link]

29. Li X & Guo B*. (2020) Substantially adaptive potential in polyploid cyprinid fishes: evidence from biogeographic, phylogenetic and genomic studies. Proceedings of the Royal Society B: Biological Sciences, 287: 20193008. [link]

28. Varadharajan S*, Rastas P, Löytynoja A, Matschiner M, Calboli FCF, Guo B, Nederbragt AJ, Jakobsen KS*, Merilä J. (2019) A high-quality assembly of the nine-spined stickleback (Pungitius pungitius) genome. Genome Biology and Evolution, 11:3291-3308. [link]

Preprint: bioRxiv, 741751. [link]

27. Wang Yingnan & Guo B*. (2019) Adaption to extreme environments: a perspective from fish genomics. Reviews in Fish Biology and Fisheries, 29:735–747. [link]

26. Guo B†, Fang B†, Shikano T, Momigliano P, Wang C, Kravchenko A, Merilä J*. (2019) A phylogenomic perspective on diversity, hybridization and evolutionary affinities in the stickleback genus Pungitius. Molecular Ecology, 28:4046-4064. [link]

25. Nielsen ES, Henriques R, Toonen RT, Knapp I, Guo B, von der Heyden S*. (2018) Complex signatures of genomic variation of two non-model marine species in a homogeneous environment. BMC Genomics, 19:347. [link]

24. Guo B*. (2017) Complex genes are preferentially retained after whole-genome duplication in teleost fish. Journal of Molecular Evolution, 84:253-258. [link]

23. Li Z*, Guo B, Yang J, Herczeg G, Gonda A, Balázs G, Shikano T, Calboli FCF, Merilä J. (2017) Deciphering the genomic architecture of the stickleback brain with a novel multi-locus gene-mapping approach. Molecular Ecology, 26:1557-1575. [link]

Commentary by Jon Slate. (2017) Robust inference of genetic architecture in mapping studies. Molecular Ecology, 26:1453-1455. [link]

22. Guo B*, Li Z, Merilä J. (2016) Population genomic evidence for adaptive differentiation in the Baltic Sea herring. Molecular Ecology, 25:3884–3900. [link]

21. Guo B, Lu D, Liao WB*, Merilä J. (2016) Genome-wide scan for adaptive differentiation along altitudinal gradient in the Andrew’s toad Bufo andrewsi. Molecular Ecology, 25:2833-2852. [link]

20. Yang J, Guo B*, Shikano T, Liu X*, Merilä J. (2016) Quantitative trait locus analysis of body shape divergence in nine-spined sticklebacks based on high-density SNP-panel. Scientific Reports, 6:26632. [link]

19. Rastas P†, Calbol FCF†, Guo B, Shikano T, Merilä J*. (2016) Construction of ultra-dense linkage maps using Lep-MAP2 as exemplified with stickleback F2 recombinant crosses. Genome Biology and Evolution, 8:78-93. [link]

Selected as cover story. [link]

18. Guo B, Shikano T, Vukic J, Sanda R, Merilä J*. (2016) Complete mitochondrial genome of the Ukrainian nine-spined stickleback Pungitius platygaster (Gasterosteiformes, Gasterosteidae). Mitochondrial DNA Part B: Resources, 1:68-69. [link]

17. Guo B, Shikano T, Wang C, Merilä J*. (2016) Complete mitochondrial genome of the smoot-tailed nine-spined stickleback Pungitius laevis (Gasterosteiformes, Gasterosteidae). Mitochondrial DNA Part B: Resources, 1:70-71. [link]

16. Guo B, Toli E, Merilä J*. (2016) Complete mitochondrial genome of the nine-spined stickleback Pungitius pungitius (Gasterosteiformes, Gasterosteidae). Mitochondrial DNA Part B: Resources, 1:72-73. [link]

15. Shikano T, Guo B, Vukic J, Sanda R, Merilä J*. (2016) Complete mitochondrial genome of the Greek nine-spined stickleback Pungitius hellenicus (Gasterosteiformes, Gasterosteidae). Mitochondrial DNA Part B: Resources, 1:66-67. [link]

14. Shikano T, Guo B, Merilä J*. (2016) Complete mitochondrial genome of the Shakhalin nine-spined stickleback Pungitius tymensis (Gasterosteiformes, Gasterosteidae). Mitochondrial DNA Part B: Resources, 1:74-75. [link]

13. Guo B*, DeFaveri J, Sotelo G, Nair A, Merilä J. (2015) Population genomic evidence for adaptive differentiation in Baltic Sea three-spined sticklebacks. BMC Biology, 13:19. [link]

12. Zou M*, Guo B, Ma X. (2014) Characterizing the transcriptome of yellow-cheek carp (Elopichthys bambusa) enables evolutionary analyses within endemic East Asian Cyprinidae. Gene, 547:267-272. [link]

11. Guo B*, Chain FJ, Bornberg-Bauer E, Leder EH, Merilä J. (2013) Genomic divergence between nine- and three-spined sticklebacks. BMC Genomics, 14:756. [link]

10. Guo B, Zou M, Wagner A*. (2012) Pervasive indels and their evolutionary dynamics after the fish-specific genome duplication. Molecular Biology and Evolution, 29:3005-3022. [link]

9. Zou M, Guo B, Tao W, Arratia G, He S*. (2012) Integrating multi-origin expression data improves resolution of the deep phylogeny of ray-finned fish (Actinopterygii). Scientific Reports, 2:665. [link]

8. Guo B, Wagner A, He S*. (2011) Duplicated gene evolution following whole-genome duplication in teleost Fish. Pp. 27-36. In: Felix Friedberg (Ed.), Gene Duplication. InTech, Rijeka, Croatia. [link]

7. Zou M, Guo B, He S*. (2011) The roles and evolutionary patterns of intronless genes in deuterostomes. Comparative and Functional Genomics, 2011:680673. [link]

6. Guo B, Zou M, Gan X, He S*. (2010) Genome size evolution in pufferfish: an insight from BAC clone-based Diodon holacanthus genome sequencing. BMC Genomics, 11:396. [link]

5. Guo B, Gan X, He S*. (2010) Hox genes of the Japanese eel Anguilla japonica and Hox cluster evolution in teleosts. Journal of Experimental Zoology Part B: Molecular Development and Evolution, 314:135-147. [link]

4. Guo B, Tong C, He S*. (2009) Sox genes evolution in closely related young tetraploid cyprinid fishes and their diploid relative. Gene, 439:102-112. [link]

3. Tong C, Guo B, He S*. (2009) Bead-probe complex capture a couple of SINE and LINE family from genomes of two closely related species of East Asian cyprinid directly using magnetic separation. BMC Genomics, 10:83. [link]

2. Li Z, Guo B, Li J, He S*, Chen Y. (2008) Bayesian mixed models and divergence time estimation of Chinese cavefishes (Cyprinidae: Sinocyclocheilus). Chinese Science Bulletin, 53:2342-2352. [link]

1. Guo B, Li J, Tong C, He S*. 2008. Cloning and sequence analysis of Sox genes in a tetraploid cyprinid fish, Tor douronensis. Chinese Science Bulletin, 53:1988-1995. [link]