Xin Zhou

My research asks how biodiversity originates, how organisms adapt to changing environments, and how these evolutionary processes shape ecological function. We combine biodiversity genomics, evolutionary genomics, phylogenomics and functional approaches to connect patterns observed across species and populations with the biological mechanisms that generate them.

A major focus of my current program is honey bee evolution and adaptation. Honey bees provide a tractable system for moving from evolutionary diversification to mechanism because closely related species and populations have repeatedly adapted to contrasting climates, ecological conditions and social environments. Our work examines the genomic and physiological basis of environmental adaptation, social regulation of colony function, and coevolution between hosts and their gut microbiota.

A second research pillar develops genomic approaches for discovering and interpreting biodiversity. My earlier work helped establish DNA barcoding for global freshwater insects, build regional reference libraries in Churchill, Manitoba, and advance community-scale approaches including DNA metabarcoding and PCR-free genome skimming. I am also a co-founder of the 1K Insect Transcriptome Evolution (1KITE) project, an international collaboration that has helped resolve deep relationships across the insect Tree of Life.

My Canada Research Chair program extends these approaches to ecological networks in the Subarctic. Field research in Churchill links genomic reference libraries with plant–pollinator interaction. This integrated approach examines how biodiversity, species interactions and ecological function respond to rapid environmental change. The long-term goal is to connect biodiversity discovery, evolutionary history and biological mechanism with the resilience of natural ecosystems.

• Ph.D., Entomology, Rutgers University, USA
• M.Sc., Peking University, China
• B.Sc., Peking University, China

1. Biodiversity and Evolution

We develop molecular and genomic approaches to discover biodiversity and reconstruct its evolutionary history. This work progresses from DNA barcoding of individual specimens, to metabarcoding of whole communities, PCR-free genome skimming for more quantitative biodiversity assessment, and genomic reconstruction of ecological interactions. Phylogenomics provides the historical framework needed to understand how this diversity arose. Through 1KITE and related collaborations, we have contributed to resolving deep insect relationships and the evolutionary origins of major innovations, while species-level barcode libraries extend this framework toward the organisms encountered in ecological surveys.

2. Evolutionary Diversification and Biological Mechanisms

Honey bees are a central model system for linking evolutionary pattern with biological mechanism. We investigate how repeated environmental adaptation is encoded in genomes and translated into physiology and behaviour. Current themes include the evolution of thermogenesis and climatic adaptation, genomic divergence among geographic populations, pigmentation and phenotypic plasticity, and the molecular pathways through which brood signals regulate worker physiology and colony nutritional allocation. This framework allows comparative genomics to generate mechanistic hypotheses that can be tested experimentally.

3. Host–Microbiota Coevolution

Honey bees also provide a powerful system for studying how animals evolve with their microbial partners. The core gut microbiota is conserved at broad taxonomic levels, while finer-scale bacterial lineages vary among host species and populations. Our work examines host specificity, microbial metabolism, immune regulation, cold acclimation and other functions that emerge from host–microbiota interactions. We are particularly interested in how environmental change and human management alter both host and microbial evolutionary trajectories and the consequences for colony function.

4. Pollination Networks and Ecosystem Resilience

Our field program in Churchill, Manitoba, builds on long-standing experience in northern biodiversity research. We are developing genomic reference libraries for local plants and insects and using DNA carried by pollinators to reconstruct plant–pollinator interactions. Repeated sampling across habitats and seasons will allow us to examine how Subarctic pollination networks are organized, how they vary through time, and how changes in biodiversity and interaction structure may affect ecological resilience under rapid environmental change.

• Tier 1 Canada Research Chair in Eukaryote Biodiversity Genomics, University of Guelph.
• Co-founder of the 1K Insect Transcriptome Evolution (1KITE) project, an international phylogenomics collaboration spanning all major insect lineages.
• Leadership in the Trichoptera Barcode of Life initiative, linking global DNA barcode coverage with taxonomy and species-level phylogenetic frameworks.
• Former Executive Director of the China National GeneBank at BGI; Professor at China Agricultural University.
• Long-term research experience in Churchill, Manitoba, from freshwater-insect barcode reference libraries to current Subarctic pollination-network research.

Phylogenomics

• The genomics revolution drives a new era in entomology
  Li, F., X. Wang, and X. Zhou
  2025. Annual Review of Entomology 70: 379-400.

• Phylogenomics recovers multiple origins of portable case-making in caddisflies (Insecta: Trichoptera), nature’s underwater architects
  Frandsen, P. B., R. W. Holzenthal, M. Espeland, J. Breinholt, J. A. T. Thorpe, S. Simon, A. Y. Kawahara, D. Plotkin, S. Hotaling, Y. Li, C. R. Nelson, O. Niehuis, C. Mayer, L. Podsiadlowski, A. Donath, B. Misof, E. M. Lemmon, A. Lemmon, J. C. Morse, S. Liu, S. Pauls, and X. Zhou
  2024. Proceedings of the Royal Society B: Biological Sciences 291: 20240514.

• The evolution and genomic basis of beetle diversity
  McKenna, D. D., S. Shin, D. Ahrens, M. Balke, C. Beza-Beza, D. J. Clarke, A. Donath, H. E. Escalona, F. Friedrich, H. Letsch, S. Liu, D. Maddison, C. Mayer, B. Misof, P. J. Murin, O. Niehuis, R. S. Peters, L. Podsiadlowski, H. Pohl, E. D. Scully, E. V. Yan, X. Zhou, A. Ślipiński, R. G. Beutel
  2019. Proceedings of the National Academy of Sciences USA 116(49): 24729-24737.

• Phylogenomics reveals the evolutionary timing and pattern of butterflies and moths
  Kawahara, A. Y., D. Plotkin, M. Espeland, K. Meusemann, E. F.A. Toussaint, A. Donath, F. Gimnich, P. B. Frandsen, A. Zwick, M. dos Reis, J. R. Barber, R. S. Peters, S. Liu, X. Zhou, C. Mayer, L. Podsiadlowski, C. Storer, J. E. Yack, B. Misof, J. W. Breinholt
  2019. Proceedings of the National Academy of Sciences USA 116(45): 22657-22663.

• Evolutionary history of Polyneoptera and its implications for our understanding of the early evolution of winged insects
  Wipfler, B., H. Letsch, P. B. Frandsen, P. Kapli, C. Mayer, D. Bartel, T. R. Buckley, A. Donath, J. S. Edgerly-Rooks, M. Fujita, S. Liu, R. Machida, Y. Mashimo, B. Misof, O. Niehuis, R. S. Peters, M. Petersen, L. Podsiadlowski, K. Schütte, S. Shimizu, T. Uchifune, J. Wilbrandt, E. Yan, X. Zhou, and S. Simon
  2019. Proceedings of the National Academy of Sciences USA 116(8): 3024-3029.

• Phylogenomics and the evolution of hemipteroid insects
  Johnson, K. P., C. H. Dietrich, F. Friedrich, R. G. Beutel, B. Wipfler, R. S. Peters, J. M. Allen, M. Petersen, A. Donath, K. K. O. Walden, A. M. Kozlov, L. Podsiadlowski, C. Mayer, K. Meusemann, A. Vasilikopoulos, R. M. Waterhouse, S. L. Cameron, C. Weirauch, D. R. Swanson, D. M. Percy, N. B. Hardy, I. Terry, S. Liu, X. Zhou, B. Misof, H. M. Robertson, and K. Yoshizawa
  2018. Proceedings of the National Academy of Sciences USA 115(50): 12775-12780.

• Evolutionary history of the Hymenoptera
  Peters, R. S. , L. Krogmann, C. Mayer, A. Donath, S. Gunkel, K. Meusemann, A. Kozlov, L. Podsiadlowski, M. Petersen, R. Lanfear, P. A. Diez, J. Heraty, K. M. Kjer, S. Klopfstein, R. Meier, C. Polidori, T. Schmitt, S. Liu, X. Zhou, T. Wappler, J. Rust, B. Misof, and O. Niehuis
  2017. Current Biology 27(7): 1013-1018.

• The Trichoptera barcode initiative: a strategy for generating a species-level Tree of Life
  Zhou, X., P. B. Frandsen, R. W. Holzenthal, C. R. Beet, K. R. Bennett, R. J. Blahnik, N. Bonada, D. Cartwright, S. Chuluunbat, G. V. Cocks, G. E. Collins, J. deWaard, J. Dean, O. S. Flint Jr., A. Hausmann, L. Hendrich, M. Hess, I. D. Hogg, B. C. Kondratieff, H. Malicky, M. A. Milton, J. Morinière, J. C. Morse, F. N. Mwangi, S. U. Pauls, M. R. Gonzalez, A. Rinne, J. L. Robinson, J. Salokannel, M. Shackleton, B. Smith, A. Stamatakis, R. StClair, J. A. Thomas, C. Zamora-Muñoz, T. Ziesmann, and K. M. Kjer
  2016. Philosophical Transactions of the Royal Society B: Biological Sciences 371(1702): 20160025.

• Phylogenomics resolves the timing and pattern of insect evolution
  Misof, B., S. Liu, K. Meusemann, R. S. Peters, A. Donath, C. Mayer, P. B. Frandsen, J. Ware, T. Flouri, R. G. Beutel, O. Niehuis, M. Petersen, F. Izquierdo-Carrasco, T. Wappler, J. Rust, A. J. Aberer, U. Aspöck, H. Aspöck, A. Blanke, D. Bartel, S. Berger, A. Böhm, T. Buckley, B. Calcott, J. Chen, F. Friedrich, M. Fukui, M. Fujita, C. Greve, P. Grobe, S. Gu, Y. Huang, L. S. Jermiin, A. Y. Kawahara, L. Krogmann, M. Kubiak, R. Lanfear, H. Letsch, Y. Li, Z. Li, J. Li, H. Lu, R. Machida, Y. Mashimo, P. Kapli, D. McKenna, G. Meng, Y. Nakagaki, J. L. Navarrete-Heredia, M. Ott, Y. Ou, G. Pass, L. Podsiadlowski, H. Pohl, B. M. v. Reumont, K. Schütte, K. Sekiya, S. Shimizu, A. Slipinski, A. Stamatakis, W. Song, X. Su, N. U. Szucsich, M. Tan, X. Tan, M. Tang, J. Tang, G. Timelthaler, S. Tomizuka, M. Trautwein, X. Tong, T. Uchifune, M. G. Walzl, B. Wiegmann, J. Wilbrandt, B. Wipfler, T. K. F. Wong, Q. Wu, G. Wu, Y. Xie, S. Yang, Q. Yang, D. K. Yeates, K. Yoshizawa, Q. Zhang, R. Zhang, W. Zhang, Y. Zhang, J. Zhao, C. Zhou, L. Zhou, T. Ziesmann, S. Zou, Y. Li, X. Xu, Y. Zhang, H. Yang, J. Wang, J. Wang, K. M. Kjer, and X. Zhou
  2014. Science 346(6210): 763-767.

Biodiversity Genomics

• Tracing the genealogy origin of geographic populations based on genomic variation and deep learning
  Yang, B., X. Zhou, and S. Liu
  2024. Molecular Phylogenetics and Evolution 198: 108142.

• Tracing the origin of honey products based on metagenomics and machine learning
  Liu, S., D. Lang, G. Meng, J. Hu, M. Tang, and X. Zhou
  2022. Food Chemistry 371: 131066.

• Genome-skimming provides accurate quantification for pollen mixtures
  Lang, D., M. Tang, J. Hu, and X. Zhou
  2019. Molecular Ecology Resources 19:1433-1446.

• High-throughput monitoring of wild bee diversity and abundance via mitogenomics
  Tang, M., C. Hardman, Y. Ji, G. Meng, S. Liu, M. Tan, S. Yang, E. Moss, J. Wang, C. Yang, C. Bruce, T. Nevard, S. G. Potts, X. Zhou, and D. W. Yu
  2015. Methods in Ecology and Evolution 6: 1034-1043.

• Ultra-deep sequencing enables high-fidelity recovery of biodiversity for bulk arthropod samples without PCR amplification
  Zhou, X., Y. Li, S. Liu, Q. Yang, X. Su, L. Zhou, M. Tang, R. Fu, J. Li, and Q. Huang
  2013. GigaScience 2: 4.

Evolution and Adaptation

• Convergent elevation of mitochondrial proton leakage improves thermogenesis in honeybees
  Xiao, Y., L. Qiu, H. Wang, Y. Fan, Z. Zhao, D. Wu, Z. Wang, J. Zhang, M. A. Malik, S. H. Parey, M. Tang, B. Sun, W. Du, X. Zhou, and S. Liu
  2026. Molecular Biology and Evolution 43(8): msag174.

• Temporal genomics reveal rapid adaptation to pesticide exposure in Eastern honeybees
  Liu, S., L. Qiu, D. Liang, A. T. Alby, M. S. Sinding, M. Tang, M. Z. Mustafa, F. Msalleh, C. Hou, M. T. P. Gilbert, and X. Zhou
  2026. National Science Review 13(12): nwaf438.

• Protein craving links larval signals to food provisioning in honey bees
  Li, Z., Y. Wu, J. Liu, C. Yang, S. Wang, M. Huang, S. Luo, and X. Zhou
  2026. Science Advances 12(20): eaec3855.

• Temperature-responsive spatial-temporal regulation underlies phenotypic plasticity of body pigmentation in Eastern honey bee
  Wang, S., L. Qiu, Y. Wu, Z. Li, Z. Wang, Z. Chen, S. Liu, and X. Zhou
  2026. Insect Biochemistry and Molecular Biology 186: 104454.

• The leucokinin pathway regulates honey bee sugar consumption via Piezo
  Li, Z., C. Yang, Y. Wu, X. Zhang, X. Zhou, and S. Luo
  2026. Insect Biochemistry and Molecular Biology 186: 104448.

• Drivers of genomic differentiation landscapes in populations of disparate ecological and geographical settings within mainland Apis cerana
  Dong, J., L. Qiu, X. Zhou, and S. Liu
  2024. Molecular Ecology 33: e17414.

• Defining honeybee subspecies in an evolutionary context warrants strategized conservation
  Qiu, L., J. Dong, X. Li, S. H. Parey, K. Tan, M. Orr, A. Majeed, X. Zhang, S. Luo, X. Zhou, C. Zhu, T. Ji, Q. Niu, S. Liu, and X. Zhou
  2023. Zoological Research 44(3): 483-493.

• Gene reuse facilitates rapid radiation and independent adaptation to diverse habitats in the Asian honeybee
  Ji, Y., X. Li, T. Ji, J. Tang, L. Qiu, J. Hu, J. Dong, S. Luo, S. Liu, P. B. Frandsen, X-G Zhou, S. H. Parey, L. Li, Q. Niu, and X. Zhou
  2020. Science Advances 6(51): eabd3590.

Host-Gut Microbiota Interactions

• Gut microbiota-derived butyrate primes systemic immunity in honeybees by mediating lipid metabolic reprogramming
  Liu, J., Y. Wu, Z. Li, J. Tang, X. Zhou, and S. Luo
  2026. Nature Communications 17: 2924.

• Honeybee-Gilliamella synergy in carbohydrate metabolism enhances host thermogenesis in cold acclimation
  Tang, M, C. Li, X. Ge, Y. Kuang, L. Qiu, K. C. Chan, L. Guo, Z. Chen, Z. Zhao, B. Zhang, S. Liu, and X. Zhou
  2025. npj Biofilms and Microbiomes 11: 172.

• Life history strategies complement niche partitioning to support the coexistence of closely related Gilliamella species in the bee gut
  Yang, C., B. Han, J. Tang, J. Hu, L. Qiu, W. Cai, X. Zhou, and X. Zhang
  2025. The ISME Journal 19(1): wraf016.

• Lactobacillus Firm-5-derived succinate prevents the honeybees from having diabetes-like symptoms
  Han, B., J. Hu, C. Yang, J. Tang, Y. Du, L. Guo, Y. Wu, X. Zhang, and X. Zhou
  2024. Proceedings of the National Academy of Sciences USA 121(36): e2405410121.

• Synergistic pectin deconstruction is a prerequisite for mutualistic interactions between honeybee gut bacteria
  Tang, J., W. Zuo, L. Guo, Z. Han, C. Yang, B. Han, L. Dai, X. Zhang, and X. Zhou
  2024. Nature Communications 15: 6937.

• Temporospatial dynamics and host-specificity of honeybee gut bacteria
  Luo, S., X. Zhang, and X. Zhou
  2024. Cell Reports 43(7): 114408.

• Reactive oxygen species are regulated by immune deficiency and Toll pathways in determining host-specificity of honeybee gut bacteria
  Guo, L., J. Tang, M. Tang, S. Luo, and X. Zhou
  2023. Proceedings of the National Academy of Sciences USA 120(33): e2219634120.

• Community dynamics in structure and function of honey bee gut bacteria in response to winter dietary shifts
  Li, C., M. Tang, X. Li, and X. Zhou
  2022. mBio 13(5): e01131-22.

• Significant compositional and functional variation reveals patterns of gut microbiota evolution among wide-spread Asian honeybee populations
  Su, Q. , M. Tang, J. Hu, J. Tang, X. Zhang, X. Li, Q. Niu, X. Zhou, S. Luo, and X. Zhou
  2022. Frontiers in Microbiology 13: 934459.

• ONEH*1000 – Introduction to One Health (Winter 2027)

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