Plant Functional Phylogenomics
We are developing methods for mining genomic and transcriptomic data at the macroevolutionary scale that go beyond "single-copy genes". By doing so now we are able to detect the phylogenetic and functional locations of gene tree discordance, gene and genome duplication, molecular rate heterogeneity, and natural selection at a scale that is never before possible.
Representative publications:
McKain, M.R., M.G. Johnson, S. Uribe‐Convers, D. Eaton, and Y. Yang. 2018. Practical considerations for plant phylogenomics. Applications in Plant Sciences 6(3): e1038. Open access
Yang, Y., M.J. Moore, S.F. Brockington, J. Mikenas, J. Olivieri, J.F. Walker, and S.A. Smith. 2017. Improved transcriptome sampling pinpoints 26 ancient and more recent polyploidy events in Caryophyllales, including two allopolyploidy events. New Phytologist. doi:10.1111/nph.14812
Yang, Y., M.J. Moore, S.F. Brockington, D.E. Soltis, G.K.-S. Wong, E.J. Carpenter, Y. Zhang, L. Chen, Z.-X. Yan, Y.-L. Xie, R.F. Sage, S. Covshoff, J.M. Hibberd, M.N. Nelson, and S.A. Smith. 2015. Dissecting molecular evolution in the highly diverse plant clade Caryophyllales using transcriptome sequencing. Molecular Biology and Evolution. 32(8): 2001-2014. Open access
Yang, Y. and S.A. Smith. 2014. Orthology inference in non-model organisms using transcriptomes and low-coverage genomes: improving accuracy and matrix occupancy for phylogenomics. Molecular Biology and Evolution. 31 (11): 3081–3092 Open access
McKain, M.R., M.G. Johnson, S. Uribe‐Convers, D. Eaton, and Y. Yang. 2018. Practical considerations for plant phylogenomics. Applications in Plant Sciences 6(3): e1038. Open access
Yang, Y., M.J. Moore, S.F. Brockington, J. Mikenas, J. Olivieri, J.F. Walker, and S.A. Smith. 2017. Improved transcriptome sampling pinpoints 26 ancient and more recent polyploidy events in Caryophyllales, including two allopolyploidy events. New Phytologist. doi:10.1111/nph.14812
Yang, Y., M.J. Moore, S.F. Brockington, D.E. Soltis, G.K.-S. Wong, E.J. Carpenter, Y. Zhang, L. Chen, Z.-X. Yan, Y.-L. Xie, R.F. Sage, S. Covshoff, J.M. Hibberd, M.N. Nelson, and S.A. Smith. 2015. Dissecting molecular evolution in the highly diverse plant clade Caryophyllales using transcriptome sequencing. Molecular Biology and Evolution. 32(8): 2001-2014. Open access
Yang, Y. and S.A. Smith. 2014. Orthology inference in non-model organisms using transcriptomes and low-coverage genomes: improving accuracy and matrix occupancy for phylogenomics. Molecular Biology and Evolution. 31 (11): 3081–3092 Open access
Evolution of gene families and modules
What are the mechanisms underlying trait evolution?
Gene families that we are investigating include those involved in gain and loses of betalain pigmentation and plant carnivory. We are also exploring changes in co-expression networks associated with evolution of metabolites.
Representative publications:
Lopez-Nievesa, S., Y. Yang, A. Timoneda, M.-M. Wang, T. Feng, S.A. Smith, S.F. Brockington, and H.A. Maeda. Relaxation of tyrosine pathway regulation underlies the evolution of betalain pigmentation in Caryophyllales. 2018. New Phytologist 217(2): 896–908 Link
Brockington S.F.*, Y. Yang*, F. Gandia-Herrero, S. Covshoff, J.M. Hibberd, R.F. Sage, G.K.-S. Wong, M.J. Moore and S.A. Smith. 2015. Lineage specific gene radiations underly the evolution of novel betalain pigmentation in Caryophyllales. New Phytologist. 207(4) 1170–1180 *Co-first author. Open access
Gene families that we are investigating include those involved in gain and loses of betalain pigmentation and plant carnivory. We are also exploring changes in co-expression networks associated with evolution of metabolites.
Representative publications:
Lopez-Nievesa, S., Y. Yang, A. Timoneda, M.-M. Wang, T. Feng, S.A. Smith, S.F. Brockington, and H.A. Maeda. Relaxation of tyrosine pathway regulation underlies the evolution of betalain pigmentation in Caryophyllales. 2018. New Phytologist 217(2): 896–908 Link
Brockington S.F.*, Y. Yang*, F. Gandia-Herrero, S. Covshoff, J.M. Hibberd, R.F. Sage, G.K.-S. Wong, M.J. Moore and S.A. Smith. 2015. Lineage specific gene radiations underly the evolution of novel betalain pigmentation in Caryophyllales. New Phytologist. 207(4) 1170–1180 *Co-first author. Open access
Plant Systematics
We have been working on the phylogeny, taxonomic revision, and biogeography of Euphorbia subg. Chamaesyce. With around 600 species and a worldwide distribution, the group is extraordinary in many aspects:
- Diverse growth forms: from ephemeral annual herbs to shrubs and trees; pencil-stem succulents evolved at least four times independently in both the New World and the Old World exhibiting convergent evolution.
- Euphorbia is the only plant genus with all three known photosynthesis pathways. All three types as well as intermediate forms are found in subgenus Chamaesyce. The subgenus provides an unique opportunity to study the pre-conditions and evolutionary trajectories for evolution of photosynthetic systems.
- Dramatic island radiation of woody Hawaiian Euphorbia provides unique "natural experiments" for studying plant diversification
Representative publications:
Yang, Y., C.W. Morden, M.J. Sporck-Koehler, L. Sack, P.E. Berry. Repeated range expansion and niche shift in a volcanic hotspot archipelago: radiation of Hawaiian Euphorbia (Euphorbiaceae). bioRxiv doi: http://dx.doi.org/10.1101/056580
Yang, Y., R. Riina, J.J. Morawetz, T. Haevermans, X. Aubriot and P.E. Berry. 2012. Molecular phylogenetics and classification of Euphorbiasubgenus Chamaesyce: a group with high diversity in photosynthetic systems and growth forms. Taxon 61(4):764–789 Link
Yang, Y. and P.E. Berry. 2011. Phylogenetics of the Chamaesyce clade (Euphorbia, Euphorbiaceae): reticulate evolution and long-distance dispersal in a prominent C4 lineage. American Journal of Botany 98(9):1486–1503 Link
Yang, Y., C.W. Morden, M.J. Sporck-Koehler, L. Sack, P.E. Berry. Repeated range expansion and niche shift in a volcanic hotspot archipelago: radiation of Hawaiian Euphorbia (Euphorbiaceae). bioRxiv doi: http://dx.doi.org/10.1101/056580
Yang, Y., R. Riina, J.J. Morawetz, T. Haevermans, X. Aubriot and P.E. Berry. 2012. Molecular phylogenetics and classification of Euphorbiasubgenus Chamaesyce: a group with high diversity in photosynthetic systems and growth forms. Taxon 61(4):764–789 Link
Yang, Y. and P.E. Berry. 2011. Phylogenetics of the Chamaesyce clade (Euphorbia, Euphorbiaceae): reticulate evolution and long-distance dispersal in a prominent C4 lineage. American Journal of Botany 98(9):1486–1503 Link