
Overview
Background
Bio
Dr. Yang Liu is an evolutionary geneticist, currently working at the University of Queensland (UQ) as a Research Fellow. Prior to UQ, he obtained a PhD from the University of British Columbia (UBC) and did a postdoc research at UBC and University of Cambridge. He is broadly interested in the eco-evolutionary dynamics of plant populations that have undergone environmental heterogeneity over spatiotemporal scales. The goal of his research is to increase our understanding of the impacts of major episodes in plant demography and life histories on trait evolution and to foster sustainability. He tackles research questions at the interface between ecology and evolutionary biology with the integration of population genetics and quantitative genomics to elucidate the ecological and genetic basis of phenotypic traits and biological adaptation.
Currently, he leverages available Arabidopsis natural accessions across its geographic distribution range, coupled with their genomic data, to perform common-garden and divergent selection experiments. From these he aims to dissect features of the genetic architecture of traits and to reveal their relationships to environmental conditions. He is focusing on the shoot branching phenotype and its associated traits including flowering timing.
ECO-EVO-GENOMICS TEAM
Ongoing Projects
Three PhD positions available in 2023-2025
Project 1: Unification of selection and inheritance informs adaptive potential for generations to come (Applications open in 2023; CLOSED)
Natural selection acts on phenotypes and produces immediate phenotypic effects within a generation. In this short-term process, some phenotypes are more successful than others. Use of single traits for selection analysis could generate opposing outcomes and cannot predict how selection operates on an organism. In contrast, multivariate selection in trait combinations utilizes the attribute of functional integrations to reveal how selection works in a multi-dimensional trait space. Selection is an important force driving evolution but not equal to evolution; the latter leads to changes in genetic variation. Only through assessment of the evolutionary responses of phenotypes can we understand the transmission of such selection from one generation to the next. How does selection occurring within a generation affect evolution across generations? In the project, we aim to address the question by unifying the two processes to forecast evolutionary potential in relation to selection. To that end, we partition genetic variance into components based on an experimental design, employ experimental evolution to estimate additive genetic variance-covariances (G) on quantitative scales and evaluate G-matrix evolution. We eventually hope to elucidate how populations subjected to artificial selection move along evolutionary trajectories and whether there are genetic constraints making the fitness optimum evolutionarily inaccessible.
Project 2: Genetic and ecological bases of shoot branching divergence across Arabidopsis species-wide accessions (Applications open in 2024; CLOSED)
Spatial patterns of genetic variation are shaped by environmental factors, topological features, and dispersal barriers. As a result, we often can identify population genetic structure stratified by geographic locations or ecological niches, the drivers of population isolation by distance or the environment, clinal genetic variation over space in alignment with gradually varying environment gradients, and adaptive genetic variation in relation to environmental variables. At the ecological level, assembly rules uncover the coordination of phenotypic traits along environmental clines. Tradeoffs between traits represent the consequence of environmental filters and reflect adaptation to environmental heterogeneity. For example, three fundamental adaptive strategies are delineated by a CSR theory, that is, Competitors, Stress-tolerators, and Ruderals. As such, ways of genetic and phenotypic assemblage over space and throughout time point to a role for natural selection driven by spatially varying environmental conditions to maintain genetic variation that confers natural variation in phenotypes. In this project, we focus on an important agronomic trait – shoot branching – due to its important contribution to the overall shoot architecture of a plant and being a potential target for yield optimization. We aim to dissect features of the genetic architecture of the trait and to reveal its relationships to environmental conditions. We integrate geographic, environmental, and genomic data from the 1001 Arabidopsis Genomes Project, coupled with the branching phenotype measured in selected accessions and then forecasted for the rest of the 1001 accessions using machine-learning models, to investigate the ecological relevance and genetic underpinnings of branching divergence across the Arabidopsis species-wide accessions. Our study has implications for enhancing our understanding of the genetic and ecological basis of shoot branching divergence and the potential for generating novel knowledge for improving phenotypic predictability.
Project 3: Dimensionality, modularity, and integration: Insights from the architecture features of pan-genomes, pan-transcriptome, pan-epigenomes, and pan-chromatin (applications open in 2025) Application Portal ALSO ACCEPTING EXPRESSION OF INTEREST FROM INTERNATIONAL APPLICANTS
Organisms are functionally integrated systems, where interactions among phenotypic traits make the whole more than the sum of its parts. How is a suite of traits assembled into an adaptive module? How is an intramodule rewired to form a regulatory network? What is the persistence and stability of a module under exposures to perturbations triggered by altered interactions between the response to disparate environmental conditions or between the responses of multiple traits to the same environment? What constrains modules to vary independently, reflecting the integration and canalization of evolutionary trajectories? In this project, we utilize a compilation of pan-genomes, pan-transcriptome, pan-epigenomes, and pan-chromatin resources of Arabidopsis thaliana to uncover how dimensionality, modularity, and integration are organized at different omics levels including genetic polymorphisms, structural variants, RNA isoforms, expression abundance, epigenetic imprinting, and chromatin accessibility. Ultimately, we apply such functional elements to multivariate genomic selection, in the hope of enhancing multilayered omics-enabled prediction.
Availability
- Dr Yang Liu is:
- Available for supervision
- Media expert
Fields of research
Qualifications
- Doctor of Philosophy of Population, Ecological and Evolutionary Genetics, University of British Columbia
Research impacts
Dr. Liu's research builds on prior knowledge on gene regulatory networks and knockout mutants to phenotypic divergence, whereby developing a predictive framework to increase phenotypic predictability. This new paradigm inspires investigations into deeper questions about the causes and consequences of evolutionary forces shaping widespread genetic variation in nature.
Works
Search Professor Yang Liu’s works on UQ eSpace
2023
Journal Article
Decoupling of height growth and drought or pest resistance tradeoffs is revealed through multiple common-garden experiments of lodgepole pine
Liu, Yang, Erbilgin, Nadir, Cappa, Eduardo Pablo, Chen, Charles, Ratcliffe, Blaise, Wei, Xiaojing, Klutsch, Jennifer G, Ullah, Aziz, Azcona, Jaime Sebastian, Thomas, Barb R and El-Kassaby, Yousry A (2023). Decoupling of height growth and drought or pest resistance tradeoffs is revealed through multiple common-garden experiments of lodgepole pine. Evolution, 77 (3), 893-906. doi: 10.1093/evolut/qpad004
2022
Journal Article
Multiple-trait analyses improved the accuracy of genomic prediction and the power of genome-wide association of productivity and climate change-adaptive traits in lodgepole pine
Cappa, Eduardo P., Chen, Charles, Klutsch, Jennifer G., Sebastian-Azcona, Jaime, Ratcliffe, Blaise, Wei, Xiaojing, Da Ros, Letitia, Ullah, Aziz, Liu, Yang, Benowicz, Andy, Sadoway, Shane, Mansfield, Shawn D., Erbilgin, Nadir, Thomas, Barb R. and El-Kassaby, Yousry A. (2022). Multiple-trait analyses improved the accuracy of genomic prediction and the power of genome-wide association of productivity and climate change-adaptive traits in lodgepole pine. BMC Genomics, 23 (1) 536, 1-20. doi: 10.1186/s12864-022-08747-7
2022
Journal Article
Conservation prioritization based on past cascading climatic effects on genetic diversity and population size dynamics: Insights from a temperate tree species
Liu, Yang (2022). Conservation prioritization based on past cascading climatic effects on genetic diversity and population size dynamics: Insights from a temperate tree species. Diversity and Distributions, 28 (12) 13490, 2712-2728. doi: 10.1111/ddi.13490
2022
Journal Article
Pest defences under weak selection exert a limited influence on the evolution of height growth and drought avoidance in marginal pine populations
Liu, Yang, Erbilgin, Nadir, Ratcliffe, Blaise, Klutsch, Jennifer G., Wei, Xiaojing, Ullah, Aziz, Cappa, Eduardo Pablo, Chen, Charles, Thomas, Barb R. and El-Kassaby, Yousry A. (2022). Pest defences under weak selection exert a limited influence on the evolution of height growth and drought avoidance in marginal pine populations. Proceedings of the Royal Society B: Biological Sciences, 289 (1982) 20221034, 1-9. doi: 10.1098/rspb.2022.1034
2022
Journal Article
Improving lodgepole pine genomic evaluation using spatial correlation structure and SNP selection with single-step GBLUP
Cappa, Eduardo P., Ratcliffe, Blaise, Chen, Charles, Thomas, Barb R., Liu, Yang, Klutsch, Jennifer, Wei, Xiaojing, Azcona, Jaime Sebastian, Benowicz, Andy, Sadoway, Shane, Erbilgin, Nadir and El-Kassaby, Yousry A. (2022). Improving lodgepole pine genomic evaluation using spatial correlation structure and SNP selection with single-step GBLUP. Heredity, 128 (4), 209-224. doi: 10.1038/s41437-022-00508-2
2022
Journal Article
Integrating genomic information and productivity and climate-adaptability traits into a regional white spruce breeding program
Cappa, Eduardo P., Klutsch, Jennifer G., Sebastian-Azcona, Jaime, Ratcliffe, Blaise, Wei, Xiaojing, Ros, Letitia Da, Liu, Yang, Chen, Charles, Benowicz, Andy, Sadoway, Shane, Mansfield, Shawn D., Erbilgin, Nadir, Thomas, Barb R. and El-Kassaby, Yousry A. (2022). Integrating genomic information and productivity and climate-adaptability traits into a regional white spruce breeding program. PLoS ONE, 17 (3 March) e0264549, 1-28. doi: 10.1371/journal.pone.0264549
2021
Journal Article
Correction to: Phenotypic plasticity of natural Populus trichocarpa populations in response to temporally environmental change in a common garden (BMC Evolutionary Biology, (2019), 19, 1, (231), 10.1186/s12862-019-1553-6)
Liu, Yang and El-Kassaby, Yousry A. (2021). Correction to: Phenotypic plasticity of natural Populus trichocarpa populations in response to temporally environmental change in a common garden (BMC Evolutionary Biology, (2019), 19, 1, (231), 10.1186/s12862-019-1553-6). BMC Ecology and Evolution, 21 (1) 155, 155. doi: 10.1186/s12862-021-01884-9
2021
Journal Article
Transcriptome-wide analysis of introgression-resistant regions reveals genetic divergence genes under positive selection in Populus trichocarpa
Liu, Yang and El-Kassaby, Yousry A. (2021). Transcriptome-wide analysis of introgression-resistant regions reveals genetic divergence genes under positive selection in Populus trichocarpa. Heredity, 126 (3), 442-462. doi: 10.1038/s41437-020-00388-4
2020
Journal Article
Ecological drivers of plant life-history traits: Assessment of seed mass and germination variation using climate cues and nitrogen resources in conifers
Liu, Yang and El-Kassaby, Yousry A. (2020). Ecological drivers of plant life-history traits: Assessment of seed mass and germination variation using climate cues and nitrogen resources in conifers. Ecological Indicators, 117 106517, 1-11. doi: 10.1016/j.ecolind.2020.106517
2020
Book Chapter
Techniques for Small Non-Coding RNA Analysis in Seeds of Forest Tree Species
Liu, Yang and El-Kassaby, Yousry A. (2020). Techniques for Small Non-Coding RNA Analysis in Seeds of Forest Tree Species. Plant Epigenetics and Epigenomics: Methods and Protocols. (pp. 217-225) New York, NY United States: Humana Press. doi: 10.1007/978-1-0716-0179-2_15
2019
Journal Article
Phenotypic plasticity of natural Populus trichocarpa populations in response to temporally environmental change in a common garden
Liu, Yang and El-Kassaby, Yousry A. (2019). Phenotypic plasticity of natural Populus trichocarpa populations in response to temporally environmental change in a common garden. BMC Evolutionary Biology, 19 (1) 231, 231. doi: 10.1186/s12862-019-1553-6
2019
Journal Article
A roadmap for urban evolutionary ecology
Rivkin, L. Ruth, Santangelo, James S., Alberti, Marina, Aronson, Myla F. J., de Keyzer, Charlotte W., Diamond, Sarah E., Fortin, Marie-Josée, Frazee, Lauren J., Gorton, Amanda J., Hendry, Andrew P., Liu, Yang, Losos, Jonathan B., MacIvor, J. Scott, Martin, Ryan A., McDonnell, Mark J., Miles, Lindsay S., Munshi-South, Jason, Ness, Robert W., Newman, Amy E. M., Stothart, Mason R., Theodorou, Panagiotis, Thompson, Ken A., Verrelli, Brian C., Whitehead, Andrew, Winchell, Kristin M. and Johnson, Marc T. J. (2019). A roadmap for urban evolutionary ecology. Evolutionary Applications, 12 (3), 384-398. doi: 10.1111/eva.12734
2019
Journal Article
Novel insights into plant genome evolution and adaptation as revealed through transposable elements and non-coding RNAs in conifers
Liu, Yang and El-Kassaby, Yousry A. (2019). Novel insights into plant genome evolution and adaptation as revealed through transposable elements and non-coding RNAs in conifers. Genes, 10 (3) 228, 228. doi: 10.3390/genes10030228
2018
Journal Article
Evapotranspiration and favorable growing degree-days are key to tree height growth and ecosystem functioning: Meta-Analyses of Pacific Northwest historical data
Liu, Yang and El-Kassaby, Yousry A. (2018). Evapotranspiration and favorable growing degree-days are key to tree height growth and ecosystem functioning: Meta-Analyses of Pacific Northwest historical data. Scientific Reports, 8 (1) 8228. doi: 10.1038/s41598-018-26681-1
2017
Book Chapter
Roles of the Environment in Plant Life-History Trade-offs
Liu, Yang, Walck, Jeffrey L. and El-Kassaby, Yousry A. (2017). Roles of the Environment in Plant Life-History Trade-offs. Advances in Seed Biology. (pp. 3-24) London, United Kingdom: InTech. doi: 10.5772/intechopen.70312
2017
Journal Article
Global Analysis of Small RNA Dynamics during Seed Development of Picea glauca and Arabidopsis thaliana Populations Reveals Insights on their Evolutionary Trajectories
Liu, Yang and El-Kassaby, Yousry A. (2017). Global Analysis of Small RNA Dynamics during Seed Development of Picea glauca and Arabidopsis thaliana Populations Reveals Insights on their Evolutionary Trajectories. Frontiers in Plant Science, 8 1719. doi: 10.3389/fpls.2017.01719
2017
Journal Article
Regulatory crosstalk between microRNAs and hormone signalling cascades controls the variation on seed dormancy phenotype at Arabidopsis thaliana seed set
Liu, Yang and El-Kassaby, Yousry A. (2017). Regulatory crosstalk between microRNAs and hormone signalling cascades controls the variation on seed dormancy phenotype at Arabidopsis thaliana seed set. Plant Cell Reports, 36 (5), 705-717. doi: 10.1007/s00299-017-2111-6
2017
Journal Article
Impact of temperature shifts on the joint evolution of seed dormancy and size
Liu, Yang, Barot, Sébastien, El-Kassaby, Yousry A. and Loeuille, Nicolas (2017). Impact of temperature shifts on the joint evolution of seed dormancy and size. Ecology and Evolution, 7 (1), 26-37. doi: 10.1002/ece3.2611
2017
Journal Article
Landscape of fluid sets of hairpin-derived 21-/24-nt-long small RNAs at seed set uncovers special epigenetic features in Picea glauca
Liu, Yang and El-Kassaby, Yousry A. (2017). Landscape of fluid sets of hairpin-derived 21-/24-nt-long small RNAs at seed set uncovers special epigenetic features in Picea glauca. Genome Biology and Evolution, 9 (1), 82-92. doi: 10.1093/gbe/evw283
2016
Other Outputs
Eco-evolutionary perspective on life-history traits with special emphasis on seed dormancy and its genetic basis of adaptation in conifers
Liu, Yang (2016). Eco-evolutionary perspective on life-history traits with special emphasis on seed dormancy and its genetic basis of adaptation in conifers. PhD Thesis, Graduate School, University of British Columbia. doi: 10.14288/1.0314387
Supervision
Availability
- Dr Yang Liu is:
- Available for supervision
Before you email them, read our advice on how to contact a supervisor.
Supervision history
Current supervision
-
Doctor Philosophy
Genetic and ecological bases of shoot branching divergence across Arabidopsis species-wide accessions
Principal Advisor
Other advisors: Professor Christine Beveridge
-
Doctor Philosophy
Unification of selection and inheritance informs adaptive potential for generations to come
Principal Advisor
Other advisors: Professor Mark Cooper, Associate Professor Katrina McGuigan
-
Doctor Philosophy
Molecular physiology investigation into the mechanism of how the flowering pathway impacts branching at vegetative nodes in garden pea and arabidopsis
Associate Advisor
Other advisors: Professor Christine Beveridge, Dr Elizabeth Dun
-
Doctor Philosophy
Testing the branching model predictions using mutant perturbations of populations
Associate Advisor
Other advisors: Professor Mark Cooper, Professor Christine Beveridge
Media
Enquiries
Contact Dr Yang Liu directly for media enquiries about:
- adaptive evolution
- evolutionary biology
- global change
- life histories
- quantitative genomics
Need help?
For help with finding experts, story ideas and media enquiries, contact our Media team: