Education

2004 Ph.D. in Zoology, Kunming Institute of Zoology, CAS.

1996 B.Sc. in Biochemistry, Xiamen University

Professional Experience

2008-Present Senior Researcher, Head of Laboratory of Evolutionary & Functional Genomics, Kunming Institute of Zoology, CAS.

2007-2008 Research Scientist, German Institute of Human Nutrition

2004-2006 Postdoctoral Research Fellow, University of Michigan.

Description of your research focus (100–200 words).

The Shi lab is primarily interested in the mechanisms, functional roles, and molecular compositions underlying evolutionary repeatability. We also employ AI-assisted approaches to detect evolutionary predictability from multi-dimensional, heterogeneous omics data. Our research focuses on two major areas.

I. Echolocation as an experimental system for studying evolutionary repeatability and predictability

We use echolocating mammals (e.g., bats, dolphins, and soft-furred tree mice) and their non-echolocating close relatives as model systems to investigate the origin and evolution of echolocation. Key questions include: (1) the molecular-level origin of echolocation; (2) the molecular evolutionary repeatability of echolocation; (3) the evolutionary repeatability of neural circuit adaptations underlying echolocation; and (4) the evolutionary prediction of novel echolocating species and echolocation-related genes. We employ the soft-furred tree mouse as a model organism and apply a range of experimental approaches—including omics sequencing, optogenetics, neural tracing techniques, and genetic editing—to dissect the functions of echolocation-related traits.

II. Computational and functional evolutionary genomics

Using evolutionary, genomic, and/or functional approaches, we are interested in genetic pleiotropy, fitness landscapes, gene–environment interactions, phenotypic plasticity, DNA and protein sequence evolution, evolutionary medicine, and other key topics in evolutionary biology.

1.Yunnan Revitalization Talent Support Program Top team, The mechanisms of cell-type evolution in adaptive evolution and disease pathogenesis, No. 202505AT350003, 202405AS350022, 2024.12–2027.12, Principal Investigator

2.Basic Science Center Program of the National Natural Science Foundation of China, Evolutionary Innovation and Remodeling of Key Adaptive Traits in Animals, No. 32388102, 2024.1–2028.12, Participant

3. Yunnan Revitalization Talent Support Program Science & Technology Champion Project, Systematic identification and functional dissection of cardiomyocyte polyploidization regulators in mammals, No. 202305AB350002, 2023.1–2027.12, Principal Investigator

4.Subproject of Major Program of the National Natural Science Foundation of China, Genetic and Developmental Mechanisms of Adaptive Trait Evolution in Bats, No. 32192422, 2022.1.1–2026.12.31, Principal Investigator

5.Second Tibetan Plateau Scientific Expedition and Research Program, The Second Tibetan Plateau Scientific Expedition and Research (STEP) – Task 5: Biodiversity Conservation and Sustainable Utilization, No. 2019QZKK0500, 2019.11–2024.10, Principal Investigator

Award/Honor Awarding Organization Year

The 15th Tan Jiazhen Life Science Innovation Award (2022)

First Prize , Yunnan Natural Science Award (2025)

1. Liu Q, Hua QY, He SW, Shi LY, Chen P, Ma YS, Zhang Q, Jiang XL* and Shi P*. (2025) Evidence for echolocation in Asian shrew moles. National Science Review. nwaf591, https://doi.org/10.1093/nsr/nwaf591.

2. Shi LY, Ma YS , Hua QY, Hao JJ, Zhang Q, Ye YX, Yang L, Liu Q, Chen P, Liu Z* and Shi P*. (2025) Evolutionary repeatability of chromatin accessibility in the hippocampus between echolocating bats and soft-furred tree mice. Sci China Life Sci. 68(7):2085-2093. doi: 10.1007/s11427-024-2935-7.

3. He K, Liu Q, Xu DM, Qi FY, Bai J, He SW, Chen P, Zhou X, Cai WZ, Chen ZZ, Liu Z*, Jiang XL* and Shi P*. (2021) Echolocation in soft-furred tree mice. Science. 372(6548):eaay1513. doi: 10.1126/science.aay1513.

4. Xu DM, Yang CP, Shen QS, Pan SK, Liu Z, Zhang TZ, Zhou X, Lei ML, Chen P, Yang H, Zhang T, Guo YT, Zhan XJ*, Chen YB* and Shi P*. (2021) A single mutation underlying phenotypic convergence for hypoxia adaptation on the Qinghai-Tibetan Plateau. Cell Res. 31(9):1032-1035. doi: 10.1038/s41422-021-00517-6.

5. Liu Z, Qi FY, Xu DM, Zhou X and Shi P*. (2018) Genomic and functional evidence reveals molecular insights into the origin of echolocation in whales. Sci Adv. 4(10):eaat8821.doi: 10.1126/sciadv.aat8821.

6. Zhang ZG, Xu DM, Wang L, Hao JJ, Wang JF, Zhou X,Wang WW, Qiu Q, Huang XD, Zhou JW, Long RJ*, Zhao FQ* and Shi P*. (2016) Convergent evolution of rumen microbiomes in high-altitude mammals. Curr Biol. 26(14):1873-1879. doi: 10.1016/j.cub.2016.05.012.

7. Liu Z, Qi FY, Zhou X, Ren HQ and Shi P*. (2014) Parallel sites implicate functional convergence of the hearing gene prestin among echolocating mammals. Mol Biol Evol. 31(9): 2415-2424.doi: 10.1093/molbev/msu194.

8. Zhang ZG, Geng JW, Tang XD, Fan H, Xu JC, Wen XJ, Ma ZS* and Shi P*. (2014) Spatial heterogeneity and co-occurrence patterns of human mucosal-associated intestinal microbiota. ISME J. 8(4): 881-893. doi: 10.1038/ismej.2013.185.

9. Qiu Q, Zhang GJ,….(43-coauthors) Wang J*, Shi P*, Wang J* and Liu JQ*. (2012) The yak genome and adaptation to life at high altitude. Nature Genet. 44(8): 946-949. doi: 10.1038/ng.2343.

10. Liu Z, Li GH, Huang JF, Murphy RW and Shi P*. (2012) Hearing aid for vertebrates via multiple episodic adaptive events on prestin genes. Mol Biol Evol. 29(9): 2187-2198. doi: 10.1093/molbev/mss087.