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Diversity in Wild Cotton Populations

Exploring the genetic diversity of wild cotton (Gossypium hirsutum) populations, this project aims to characterize the true distribution of wild cotton, resolve genetic relationships between wild and domesticated forms, and infer domestication history. It also evaluates the potential of wild genetic resources for sustainable crop improvement. Combining fieldwork with genomic analyses, this work highlights cotton in its natural habitat and the insights it provides for both conservation and agriculture.

Genomic conservation of Aquilaria sinensis in Hong Kong

Aquilaria sinensis (incense tree) is known for producing agarwood, a highly valuable fragrant resinous heartwood that forms when the tree is wounded or infected, and is widely used in incense, perfumes, and traditional medicine. This high commercial value has led to intense illegal harvesting, alongside habitat loss and long-term overexploitation, making the species endangered in the wild. Using genome resequencing data, this project investigates the genetic diversity of wild A. sinensis populations in Hong Kong, aiming to resolve population structure, assess genetic variation, and inform conservation strategies for this protected species.

Origins and Diversification of New Zealand Polyploid Genus Azorella

This project investigates how polyploidization drives species diversification in New Zealand’s unique alpine flora, using Azorella (Apiaceae) as a model system. Azorella in New Zealand exhibits multiple ploidy levels (4x, 6x, and 10x), making it an excellent system for studying successive rounds of whole-genome duplication and the resulting reticulate evolutionary histories in polyploid plants. Using phylogenomic approaches based on Hyb-Seq (Angiosperms353) and genome-skimming data, this study resolves species relationships, infers the origins of higher-level polyploids, and reconstructs the biogeographic history of New Zealand Azorella. Results suggest multiple independent colonization events from South America, followed by diversification shaped by polyploidy, hybridization, and introgression across New Zealand, Australia, and subantarctic regions.

Phenotypic comparison of high-altitude African accessions of Arabidopsis thaliana

African populations of Arabidopsis thaliana harbor high levels of genetic variation, providing a powerful system for studying local adaptation. By comparing A. thaliana accessions collected from different alpine mountain environments, this work investigates patterns of parallel evolution in alpine-adaptive traits and links phenotypic divergence to underlying genetic variation across environmental gradients.

Transcriptome comparison of altitudinally adapted Arabidopsis lyrata populations

Local adaptation can be understood through phenotypic and genomic variation, where gene expression provides a key link between genotype and environment. Using a reciprocal transplant experiment in Arabidopsis lyrata, this study compares transcriptomes across populations and environments to assess expression divergence, identify differentially expressed genes, and infer biological functions associated with local adaptation across contrasting alpine sites in Norway.

publications

McLay, T. G., Birch, J. L., Gunn, B. F., Ning, W., Tate, J. A., Nauheimer, L., … & Jackson, C. J. (2021). New targets acquired: Improving locus recovery from the Angiosperms353 probe set. Applications in Plant Sciences, 9(7), e11420. Download Paper

Hämälä, T., Ning, W., Kuittinen, H., Aryamanesh, N., & Savolainen, O. (2022). Environmental response in gene expression and DNA methylation reveals factors influencing the adaptive potential of Arabidopsis lyrata. eLife, 11:e83115. Download Paper

Ning, W., Meudt, H. M., & Tate, J. A. (2024). A roadmap of phylogenomic methods for studying polyploid plant genera. Applications in Plant Sciences, e11580. Download Paper

Ning, W., Rogers, K. M., Hsu, C. Y., Magbanua, Z. V., Pechanova, O., Arick, M. A., … Grover, C. E., & Wendel, J. F. (2024). Origin and diversity of the wild cottons (Gossypium hirsutum) of Mound Key, Florida. Scientific Reports, 14(1), 14046. Download Paper

Meudt, H. M., Pearson, S. M., Ning, W., Prebble, J. M., & Tate, J. A. (2025). Forget-me-not phylogenomics: Improving the resolution and taxonomy of a rapid island and mountain radiation in Aotearoa New Zealand (Myosotis; Boraginaceae). Molecular Phylogenetics and Evolution, 204, 108250. Download Paper

Ning, W., Meudt, H. M., Nicolas, A. N., Plunkett, G. M., Heenan, P. B., Lee, W. G., & Tate, J. A. (2025). Resolving reticulate evolutionary histories of polyploid species of Azorella (Apiaceae) endemic to New Zealand. Molecular Phylogenetics and Evolution, 108469. Download Paper

Ning, W., Hu, G., Yuan, D., Arick, M. A., Hsu, C. Y., Magbanua, Z. V., … & Wendel, J. F. (2026). Comparative population genomics of relictual Caribbean island Gossypium hirsutum. Molecular Ecology, 35(2), e70239. Download Paper

Ning, W., Kayal, E., Wendel, J. F., Hsu, C. Y., Magbanua, Z. V., Pechanova, O., … & Grover, C. E. (2026). Population genomics informs conservation strategies for critically endangered Kokia species in Hawaiʻi. Ecology and Evolution, 16(4), e73104. Download Paper

Ning, W., Arick, M. A., Udall, J. A., Hsu, C. Y., Abdala-Roberts, L., Solís-Rodríguez, U., … & Wendel, J. F. (2026). Genomic diversity and the domestication history of cotton (Gossypium hirsutum). Proceedings of the National Academy of Sciences, 123(21), e2607107123. Download Paper