An integrated study of continental-scale colonization of the Eurasian Tree Sparrow

The global warming affects the environmental conditions for all species on Earth. While some can cope with this, others run the risk of local or global extinction. To better understand how wild species adapt to environmental change is a vital challenge for evolutionary genetics, ecology, and conservation biology.

Project overview

Project period: 2022 - Ongoing

Participating departments from the museum: Department of Bioinformatics and Genetics

Human-induced activities are the primary drivers of environmental change and global biodiversity loss in the Anthropocene. As the effects of human activities become more profound, it is of great importance to understand how organisms respond to changes in the environment. Identifying what factors that drive adaptation can be made by analysing genomic and phenotypic variation in a single species with a continental-wide distribution.

Project description

The Eurasian Tree Sparrow (Passer montanus), a well-known human commensal bird, is distributed across Eurasia, as well as in parts of United States and Australia to where it was introduced in the 19th century. The tree sparrow occurs in a variety of environments and is locally adapted to vastly different ecological niches. In the project, I apply an integrative approach of comparative genomics, transcriptomics and phenotypic changes to study these adaptations at a continental scale.

In an earlier project, I have successfully identified genomic mechanisms behind observed differences in body shape, beak shape and muscle phenotypes of tree sparrows living at very high elevations (>3000 m a.s.l.) with those in individuals living at low elevations. This work is now expanded to include tree sparrows from all parts of its distribution. I thus have sequenced genomes of more than 400 tree sparrows sampled across Eurasia, as well as in United States and Australia.

By leveraging a chromosome-level, high-quality genome of the tree sparrow, I am especially focusing on the relative roles of human commensalism, environmental heterogeneity and human introduction in genetic adaptation, transcriptomic regulation and phenotypic change. Research on this unique study system provides novel insights into how animals respond to human-induced environmental changes, and, even more importantly, the mechanisms underlying why some species adapt more successfully than others.

A schematic plot showing project design, research topics and methods.

Funding

Swedish Research Council
The National Science Foundation of China

Selected publications

Chen, Y., Jiang, Z., Fan, P., Ericson, P. G. P., Song, G., Luo, X., Lei, F. & Qu, Y. (2022). The combination of genomic offset and niche modelling provides insights into climate change-driven vulnerability. Nature Communications, 13, doi:10.1038/s41467-022-32546-z External link.
Qu, Y., Chen, C., Chen, X., Hao, Y., She, H., Wang, M., Ericson, P. G. P., Lin, H., Cai, T., Song, G., Ma, C., Zhang, H., Li, J., Liang, L., Wu, T., Zhao, J., Gao, Q., Zhang, G., Zhai, W., Zhang, C., Zhang, Y. & Lei, F. (2021). The evolution of ancestral and species-specific adaptations in snowfinches at the Qinghai-Tibet Plateau. Proceedings of the National Academy of Sciences, USA, 118, e2012398118. doi:10.1073/pnas.2012398118 External link.
Ericson, P. G. P., Irestedt, M., Nylander, J. A. A., Christidis, L., Joseph, L. & Qu, Y. (2020). Parallel evolution of bower-building behavior in two groups of bowerbirds suggested by phylogenomics. Systematic Biology, 69, ss. 820-829. doi:10.1093/sysbio/syaa040 External link.
Qu, Y., Chen, C., Xiong, Y., She, H., Zhang, Y., Cheng, Y., DuBay, S., Li, D., Ericson, P. G. P., Hao, Y., Wang, H., Zhao, H., Song, G., Zhang, H., Zhang, C., Yang, T., Liang, L., Wu, T., Zhao, J., Gao. Q., Zhai, W. & Lei, F. (2019). Rapid phenotypic evolution with shallow genomic differentiation during early stages of high elevation adaptation in Eurasian Tree Sparrows. National Science Review, 7, ss. 113-127. doi:10.1093/nsr/nwz138 External link.
Hao, Y., Xiong, Y., Cheng, Y., Song, G., Jia, C., Qu, Y. & Lei, F. (2019). Comparative transcriptomics of 3 high-altitude passerine birds and their low-altitude relatives. Proceedings of the National Academy of Sciences, USA, 116, ss. 11851-11856. doi:10.1073/pnas.1819657116 External link.
Qu, Y., Tian, S., Han, N., Zhao, H., Gao, B., Fu, J., Cheng, Y., Song, G., Ericson, P. G. P., Wang, D., Quan, Q., Jiang, Z., Li, R., Lei, F. & Zhang, Y. (2015). Genetic responses to seasonal variation in altitudinal stress: whole-genome resequencing of great tit in eastern Himalayas. Scientific Reports, 5, 14256. doi:10.1038/srep14256 External link.
Qu, Y., Zhao, H. W., Han, N., Zhou, G., Song, G., Gao, B., Tian, S., Zhang, J., Zhang, R., Meng, X., Zhang, Y., Zhang, Y., Zhu, Y., Wang, W., Lambert, D., Ericson, P. G. P., Subramanian, S., Yeung, C., Zhu, H., Jiang, Z., Li, R. & Lei, F. (2013). Ground tit genome reveals avian adaptation to living at high altitudes in the Tibetan plateau. Nature Communications, 4, 2071. doi:10.1038/ncomms3071 External link.