Lab members highlighted in bold

2021 and in progress

28. Morales-Briones, D.F., B. Gehrke, C.-H. Huang, A. Liston, H. Ma, H.E. Marx, D.C. Tank, Y. Yang. Analysis of paralogs in target enrichment data pinpoints multiple ancient polyploidy events in Alchemilla s.l. (Rosaceae). In revision. bioRxiv

27. Thompson, C.L.,  M. Alberti, S. Barve, F.U. Battistuzzi, J.L. Drake, L. Govaert, C. Partridge, Y. Yang. Back to the future: Reintegrating biology to understand how past eco-evolutionary change can predict future outcomes. In revision.
  • White paper from the NSF Reintegrating Biology Jumpstart meeting December 2019

26. Qiu, Y.-J., Y. Yang, C.D. Hirsch, E. Watkins. Building a reference transcriptome for the hexaploid Hard Fescue turfgrass (Festuca brevipila) using a combination of PacBio IsoSeq and Illumina sequencing. In revision. bioRxiv

25. Morales-Briones, D.F., G. Kadereit, D.T. Tefarikis, M.J. Moore, S.A. Smith, S.F. Brockington, A. Timoneda, W.C. Yim, J.C. Cushman, and Y. Yang. Disentangling sources of gene tree discordance in phylogenomic datasets: Testing ancient hybridizations in Amaranthaceae s.l. Systematic Biology. In press Open Access
  • Ancient and rapid radiations can be difficult to resolve. We present a case where commonly used methods for detecting reticulate evolution are unable to distinguish ILS, uninformative gene trees, versus true reticulation events, even with genome scale data.
  • Our results support a broadly circumscribed Amaranthaceae s.l. that includes Chenopodiaceae.
Did 2020 actually happen?
2019
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24. Qiu, Y.-J., C.D. Hirsch, Y. Yang, and E. Watkins. Towards improved molecular identification tools in Fine Fescue (Festuca L., Poaceae) turfgrasses: Nuclear genome size, ploidy, and chloroplast genome sequencing. ​Frontiers in Genetics.10:1223. Open Access

23. Chen L.-Y., D.F. Morales-Briones, C.N. Passow, and Y. Yang. Performance of gene expression analyses using de novo assembled transcripts in polyploid species. Bioinformatics. 35(21): 4314–4320. Link 
  • ​De novo transcriptome assembly is error-prone, and any downstream analysis is probably worse, especially in plants where polyploidy is common. But how bad it is? We found that unless the polyploidy event happened less than ~10 or so million years ago, gene expression analyses using de novo assembled transcriptomes are actually not that bad.

22. Feng T., Y. Yang, L. Busta, E.B. Cahoon, H.-C. Wang, and S.-Y. Lü. FAD2 Gene radiation and positive selection contributed to polyacetylene metabolism evolution in Campanulids. Plant Physiology. 181(2):714–728. Open Access

21. Wang N., Y. Yang, M.J. Moore, S.F. Brockington, J.F. Walker, J.W. Brown, B. Liang, T. Feng, C. Edwards, J. Mikenas, J. Olivieri, V. Hutchison, A. Timoneda, T. Stoughton, R. Puente, L.C. Majure, U. Eggli, and S.A. Smith. Evolution of Portulacineae marked by gene tree conflict and gene family expansion associated with adaptation to harsh environments. Molecular Biology and Evolution. 36(1): 112–126. Link
2018
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​20. Yang, Y., C.W. Morden, M.J. Sporck-Koehler, L. Sack, W.L. Wagner, and P.E. Berry. Repeated range expansion and niche shift in a volcanic hotspot archipelago: radiation of C4 Hawaiian Euphorbia (Euphorbiaceae). Ecology and Evolution. doi:10.1002/ece3.4354 Open access
  • Final chapter of Ya's Ph.D. dissertation. Ya spent two years cloning low-copy nuclear genes but got very little resolution. Allopolyploidy, rapid radiation, hybridization, and non-monophyly of morphologically well-defined unites--all the taxonomic challenges in one small clade. Nonetheless some interesting patterns emerged from chloroplast markers. ​​

​​19. ​Walker, J.F., Y. Yang, T. Feng, A. Timoneda, J. Mikenas, V. Hutchison, C. Edwards, N. Wang, S. Ahluwalia, J. Olivieri, N. Walker-Hale, L.C. Majure, R. Puente, G. Kadereit, M. Lauterbach, U. Eggli, H. Flores-Olvera, H. Ochoterena, S.F. Brockington, M.J. Moore, and S.A. Smith. From cacti to carnivores: Improved phylotranscriptomic sampling and hierarchical homology inference provides further insight to the evolution of Caryophyllales. American Journal of Botany. 105(3):446–462 Open access
  • Our Caryophyllales "capstone" paper with >300 transcriptomes

18. McKain, M.R., M.G. Johnson, S. Uribe‐Convers, D. Eaton, and Y. Yang. Practical considerations for plant phylogenomics. Applications in Plant Sciences 6(3): e1038. Open access
  • Invited review in the "Methods for Exploring the Plant Tree of Life" special issue. Ya wrote the part on transcriptome.

17. 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. New Phytologist 217(2): 896–908 Link
​16. Yang, Y., M.J. Moore, S.F. Brockington, J. Mikenas, J. Olivieri, J.F. Walker, and S.A. Smith.  Improved transcriptome sampling pinpoints 26 ancient and more recent polyploidy events in Caryophyllales, including two allopolyploidy events. New Phytologist. 217(2): 855–870 doi:10.1111/nph.14812
  • Polyploidy, both ancient and more recent ones, are more common than we previously thought. 
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​15. Smith, S.A., J.W. Brown, Y. Yang, R. Bruenn, C.P. Drummond, S.F. Brockington, J.F. Walker, N. Last, N.A. Douglas, and M.J. Moore. Disparity, diversity, and duplications in the Caryophyllales. New Phytologist 217(2): 836–854​ doi:10.1111/nph.14772​​
2017

14. Walker, J.F., Y. Yang, M.J. Moore, J. Mikenas, A. Timoneda, S.F. Brockington, and S.A. Smith. Widespread paleopolyploidy, gene tree conflict, and recalcitrant relationships among the carnivorous Caryophyllales. American Journal of Botany. 104(6): 858–867 Open access
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13. Yang, Y., M.J. Moore, S.F. Brockington, A. Timoneda, T. Feng, H. E. Marx, J. F. Walker, and S.A. Smith. An efficient field and laboratory workflow for plant phylotranscriptomic projects. Applications in Plant Sciences 5(3): 1600128. Open access
  • ​Ya put put some protocols together while wrapping up and leaving Michigan. Nicely complemented by contribution from Hannah Marx following a conversation at a BSA meeting. 
2013–2016 (during postdoc in Smith Lab, University of Michigan)

12. Berry, P.E., J.A. Peirson, J.J. Morawetz, V.W. Steinmann, R. Riina, Y. Yang, D. Geltman, and N.I. Cacho. 2016. Euphorbia. Flora of North America Editorial Committee, eds. Flora of North America North of Mexico. Vol. 12. 240–324. New York and Oxford.
  • The floristic component of Ya's dissertation. Ya wrote the treatment for 16 Euphorbia taxa after measuring and annotating over 1000 Euphorbia specimens from around the country. 

11. Smith, S.A., M.J. Moore, J.W. Brown and Y. Yang. 2015. Analysis of phylogenomic datasets reveals conflict, concordance, and gene duplications with examples from animals and plants. BMC Evolutionary Biology. 15:150. doi:10.1186/s12862-015-0423-0 Open access
  • Nice representation of gene tree conflicts mapped onto a species tree. 

​10. 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 Commentary by David L. Des Marais
  • Sam came up with the idea, Ya built the tree in a few hours, and Sam wrote the paper in a few weeks. We got super excited about the power of gene tree analyses using transcriptomes.

9. 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
  • A lot of work and novel ideas went into this paper. Working on this was the highlight of Ya's postdoc work. 

8. Horn, J.W., Z.-X. Xi, R. Riina, J.A. Peirson, Y. Yang, B.L. Dorsey, P.E. Berry, C.C. Davis, and K.J. Wurdack. 2014. Evolutionary bursts in the Euphorbia (Euphorbiaceae) are linked with photosynthetic pathway. Evolution. 68(12): 3485–3504 Link
  • A nice survey of 13C values, mapped onto the Euphorbia phylogeny. 

7. 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
  • We started playing with orthology inference softwares while waiting for 1KP to grant us data access. We ended up write some scripts ourselves and published it as a separate work. 

6. Yang, X.-X, Y. Yang, C.-J. Ji, T. Feng, Y. Shi, L. Lin, J.-J. Ma, & J.-S. He. 2014. Large-scale patterns of stomatal traits in Tibetan and Mongolian grassland species. Basic and Applied Ecology 15(2):122–132 Link
  • Work from Ya's undergraduate thesis. Lots of leaf epidermal peels and microscopy. 

5. Yang, Y. and S.A. Smith. 2013. Optimizing de novo assembly of short-read RNA-seq data for phylogenomics. BMC Genomics 14:328. doi:10.1186/1471-2164-14-328 Open access
  • Ya played with transcriptome assembly and de Bruijn graph (or attempted to) while learning Python during the first few month of postdoc work.
2012 and earlier (during graduate school in Berry Lab, University of Michigan)

4. Yang, Y., R. Riina, J.J. Morawetz, T. Haevermans, X. Aubriot and P.E. Berry. 2012. Molecular phylogenetics and classification of Euphorbia subgenus Chamaesyce: a group with high diversity in photosynthetic systems and growth forms. Taxon 61(4):764–789 Link
  • Taxonomic treatment for a 600-species clade with extraordinary morphological variation and worldwide distribution. The "ancestral Euphorbia growth form" became my avatar. 

3. 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
  • Main chapter of Ya's Ph.D. dissertation.

2. Berry, P. E., V. Steinmann, and Y. Yang. 2011. Proposal to conserve the name Euphorbia acuta  Engelm. against Euphorbia acuta Bellardi ex Colla (Euphorbiaceae). Taxon 60(2): 603–604 Link

1. Hendry, T.A., B. Wang, Y. Yang, E.C. Davis, J.E. Braggins, R.M. Schuster, & Y.-L. Qiu.2007. Evaluating phylogenetic positions of four liverworts from New Zealand, Neogrollea notabilis, Jackiella curvata, Goebelobryum unguiculatum and Herzogianthus vaginatus, using three chloroplast genes. The Bryologist 110: 738–751 Link
  • While the Berry Lab was under renovation Ya spent some time working with Yin-Long Qiu on bryophytes and learning molecular techniques from the then lab manager Tory Hendry