Genome Evolution & Phylogenetics
Large-scale genomic data to resolve relationships among species and to understand how genome rearrangements and duplications drive diversity and adaptation.
Postdoctoral Fellow · University of Michigan
Yang Li
Department of Ecology and Evolutionary Biology
Ann Arbor, Michigan, USA
I am a Postdoctoral Fellow at the University of Michigan, working with Prof. Jianzhi Zhang. I use computational biology to study the mechanisms and processes that shape biological evolution. I am always happy to discuss collaborations, so feel free to get in touch.
Research
Fitness Landscapes
Landscape navigability, accessibility of high peaks, epistasis, and the adaptive walks that determine evolutionary trajectories.
Horizontal Gene Transfer
How foreign genes enter, integrate, and adapt within host genomes, and how these transfers reshape genomic diversity and the tree of life.
News
-
New paper in EMBO Journal on a horizontally transferred bacterial gene in parasitoid wasp venom secretion.
-
New paper in Science Advances on behavioral fever in fruit flies against parasitoid wasps.
-
New paper in Molecular Biology and Evolution on reaching high peaks in fitness landscapes.
-
New paper in Genome Research on the transcriptomic and proteomic effects of gene deletion.
-
Received the Outstanding Doctoral Dissertation Award of Zhejiang Province.
-
Received the UMPDA Travel Award.
-
Attended the SMBE annual meeting in Mexico.
-
Started as a Postdoctoral Fellow at the University of Michigan.
-
Graduated as an Outstanding Graduate of Zhejiang Province (top 1%).
-
New paper in Cell on widespread horizontal gene transfer in insects.
Publications
2026
A bacterial gene acquired by parasitoid wasps contributes to venom secretion against host defence
EMBO Journal, 2026 · PDF
Key findings
- Systematic identification of 19 horizontally acquired genes in five Leptopilina parasitoid wasps.
- A prokaryotic-type gene, PTCDS, transferred from Rickettsiaceae bacteria, is required for proper venom storage in L. heterotoma and L. syphax.
- PTCDS acts in venom gland cells to regulate vesicle-mediated venom secretion, suppressing the host encapsulation response.
2025
Fruit flies exploit behavioral fever as a defense strategy against parasitic insects
Science Advances, 2025 · PDF
Key findings
- First documented case of behavioral fever against a macroparasite, observed in fruit flies infected by parasitoid wasps.
- Fever depends on upregulation of Hsp70 genes; loss of Hsp70 abolishes it, while overexpression triggers heat-seeking.
- Higher temperatures kill wasp larvae by disrupting their gut microbiota through host antimicrobial peptides.
- Shows how ectotherms use behavior to strengthen immunity against macroparasites.
On the probability of reaching high peaks in fitness landscapes by adaptive walks
Molecular Biology and Evolution, 2025 · PDF
Key findings
- The probability of reaching high peaks (PHP) varies widely across empirical and theoretical fitness landscapes.
- Ruggedness strongly shapes PHP; smoother landscapes make high peaks easier to reach.
- Higher peaks tend to have larger basins, but this alone does not guarantee a high PHP.
- Empirical landscapes do not consistently show higher PHP than Rough Mount Fuji models.
Transcriptomic and proteomic effects of gene deletion are not evolutionarily conserved
Genome Research, 2025 · PDF
Key findings
- Deleting orthologous genes in different yeasts produces distinct transcriptomic and proteomic changes.
- Expression levels themselves are conserved, but deletion effects depend on genetic background.
- Most molecular effects of a deletion are byproducts and say little about the gene's actual function.
2023
FoxO and rotund form a binding complex governing wing polyphenism in planthoppers
iScience, 2023 · PDF
Key findings
- rotund is differentially expressed between long- and short-winged brown planthoppers.
- Knocking down rotund turns long wings into intermediate wings.
- Binding to the transcription factor FoxO inhibits rotund activity.
How has horizontal gene transfer shaped the evolution of insect genomes?
Environmental Microbiology, 2023 · PDF
Key findings
- Reviews the growing genomic evidence for horizontal gene transfer in insects.
- Discusses what remains unknown about its overall extent and underlying mechanisms.
2022
Horizontal gene transfer is widespread in insects and contributes to male courtship in lepidopterans
Cell, 2022 · PDF
Key findings
- Genome-scale screen for horizontal gene transfer across 218 insect genomes.
- Lepidopterans carry, on average, the most horizontally acquired genes.
- Intron gains from host genomes likely helped foreign genes adapt.
- A horizontally acquired gene enhances male courtship behavior in moths.
2021
BmNPV-induced hormone metabolic disorder in silkworm leads to enhanced locomotory behavior
Developmental & Comparative Immunology, 2021 · PDF
Key findings
- BmNPV triggers a heat-shock response and severe brain pathology.
- Infection disrupts host hormone homeostasis.
- 20E and dopamine act in opposition to regulate virus-induced hyperactivity.
2020
Bombyx mori nucleopolyhedrovirus Bm46 is essential for efficient production of infectious BV and nucleocapsid morphogenesis
Virus Research, 2020 · PDF
Key findings
- Bm46 is not a baculovirus core gene but is pivotal late in infection.
- Deleting Bm46 lowers budded virus production without affecting viral DNA replication.
- Bm46 is required for proper nucleocapsid assembly; VP39 mislocalizes without it.
Bombyx mori nucleopolyhedrovirus F-like protein Bm14 is a factor for viral-induced cytopathic effects via regulating oxidative phosphorylation and cellular ROS levels
Virology, 2020 · PDF
Key findings
- Bm14 is a viral factor behind BmNPV-induced cytopathic effects.
- Deleting Bm14 activates oxidative phosphorylation and lowers ROS levels.
Identification of a functional region in Bombyx mori nucleopolyhedrovirus VP39 that is essential for nuclear actin polymerization
Virology, 2020 · PDF
Key findings
- Deleting vp39 abolishes nuclear actin polymerization; repairing it restores polymerization.
- Residues 192–286 in the C-terminal region of VP39 are essential for this function.
Dynamic chromatin accessibility profiling reveals changes in host genome organization in response to baculovirus infection
PLOS Pathogens, 2020 · PDF
Key findings
- BmNPV infection progressively opens host chromatin and pushes the host genome to the nuclear periphery.
- Infection-induced accessible regions carry facultative heterochromatin marks.
Honors & Awards
-
Outstanding Doctoral Dissertation of Zhejiang Province top 0.1%
-
Outstanding Doctoral Dissertation of Zhejiang University top 1%
-
UMPDA Travel Award, University of Michigan
-
Outstanding Graduate of Zhejiang Province top 1%
-
Outstanding Graduate of Zhejiang University top 5%
-
President Chu Kochen Scholarship, the highest honor of Zhejiang University 12 graduate students per year
-
National Scholarship for Graduate Students top 1%
-
Zhejiang University Excellent PhD Research Fellowship top 1%
Education & Positions
-
Postdoctoral Fellow
University of Michigan, Ann Arbor, USA -
Ph.D.
Zhejiang University, Hangzhou, China -
B.S.
Wuhan Polytechnic University, Wuhan, China