Diversity of eukaryotics is far greater than most people realize. In the Yuanning-Li lab, we are trying to use DNA records to study patterns and process of eukaryotic evolution on different time scales and with different types of genomic information. Combining a molecular systematic and/or genomic approach with information from organismal evolution has proved a powerful approach to study everything from the origin of major eukaryotic lineages (especially for marine invertebrates and fungi) to the recent adaptation to deep-sea chemosynthetic environments. Research in the lab focuses on utilizing computational approaches and genome-scale data to gain insight into molecular phylogenetics, evolutionary biology, comparative genomics, and bioinformatics.
Citations are available at Google Scholar. Lab members are indicated in bold. # co-first author, * corresponding author.
Preprints/Submitted articles
2.Feng, B.#, Yo. Li#, H. Liu#, J. L. Steenwyk, K. T. David, X. Tian, B. Xu, C. Goncalves, D. A. Opulente, A. L. LaBella, M.-C. Harrison, J. F. Wolters, S. Shao, Z. Chen, K. J. Fisher, M. Groenewald, C. T. Hittinger, X.-X. Shen, A. Rokas*, X. Zhou*, Y. Li*. Unique trajectory of gene family evolution from genomic analysis of nearly all known species in an ancient yeast lineage.
Link
1.Liu, H.#, Steenwyk JL#, Schultz D, Kocot KM, Zhou X, Shen XX, Zhao T, Rokas A.*, Li Y*. A genome-scale Opisthokonta tree of life: toward phylogenomic resolution of ancient divergences.
Research articles
2024
33.Opulente#, D. A., A. L. LaBella#, M.-C. Harrison, J. F. Wolters, C. Liu, Y. Li, J. Kominek, J. L. Steenwyk, H. R. Stoneman, J. VanDenAvond, C. R. Miller, Q. K. Langdon, M. Silva, C. Goncalves, E. J. Ubbelohde, Y. Li, K. V. Buh, M. Jarzyna, M. A. B. Haase, C. A. Rosa, N. Cadez, D. Libkind, J. H. DeVirgilio, A. B. Hulfachor, C. P. Kurtzman, J. P. Sampaio, P. Goncalves, X. Zhou, X.-X. Shen, M. Groenewald, A. Rokas*, & C. T. Hittinger*. 2024.
Genomic factors shape carbon and nitrogen metabolic niche breadth across Saccharomycotina yeasts. Science. PDF
2023
32.Steenwyk JL, Y. Li, X. Zhou, XX Shen, Rokas A.*2023.
Incongruence in the phylogenomics era. Nature Reviews Genetics. 27:1-7 PDF
31.M. Groenewald*, C.T. Hittinger, K. Bensch, D.A. Opulente, X.-X. Shen, Li Y., C. Liu, A.L. LaBella, X. Zhou, S. Limtong, S. Jindamorakot,
P. Gonçalves, V. Robert, K.H. Wolfe, C.A. Rosa, T. Boekhout, N. Čadež, G. Péter, J.P. Sampaio, M.-A. Lachance, A.M. Yurkov, H.-M. Daniel, M. Takashima, K. Boundy-Mills, D. Libkind, K. Aoki, T. Sugita, A. Rokas.
2023. A genome-informed higher rank classification of the biotechnologically important fungal subphylum Saccharomycotina. Studies in Mycology. PDF
2022
30.Li Y.,* Liu H., Steenwyk JL, LaBella AL, Harrison MC, Groenewald M, Zhou X, Shen XX, Zhao T, Hittinger CT, Rokas A.* 2022. Contrasting modes of macro and microsynteny evolution in a eukaryotic subphylum. Current Biology 29:S0960-9822(22)01670-0. PDF
29.Steenwyk JL,* Goltz DC, Buida TJ III, Li Y., Shen XX, Antonis Rokas.* 2022. OrthoSNAP: A tree splitting and pruning algorithm for retrieving single-copy orthologs from gene family trees. PLOS Biology 20(10): e3001827. PDF
28.Li Y., Altamia MA., Shipway JR., Brugler MR., Bernardino AF., de Brito TL., Lin Z., da Silva Oliveira FA., Sumida P., Smith CR., Trindade-Silva A, Halanych KM.*, Distel DL.* 2022. Contrasting Modes of Mitochondrial Genome Evolution in Sister Taxa of Wood-Eating Marine Bivalves (Teredinidae and Xylophagaidae). Genome Biology and Evolution 14(6):evac089. PDF
27.He C., Liu J.*, Wang R., Li Y., Zheng Q., Jiao F., He C., Shi Q., Xu Y., Zhang R., Thomas H., et al. 2022. Metagenomic evidence for the microbial transformation of carboxyl-rich alicyclic molecules: A long-term macrocosm experiment. Water Research 216, 118281. PDF
26.Steenwyk, J. L.*, T. J. Buida III, C. Goncalves, D. C. Goltz, G. H. Morales, M. E. Mead, A. L. LaBella, C. M. Chavez, J. E. Schmitz, M. Hadjifrangiskou, Y. Li, & A. Rokas*. 2022. BioKIT: a versatile toolkit for processing and analyzing diverse types of sequence data. Genetics 221(3):iyac079. PDF
25.Liu D., Chen J., Wang Y., Meng Y., Li Y., Huang R., Xia Y., Liu H., Jiao N., Xun L., Liu J.* 2022. Synechococcus sp. PCC7002 Uses Peroxiredoxin to Cope with Reactive Sulfur Species Stress. Mbio e01039-22. PDF
2021
24.Li Y., Shen X.-X., Evans B., Dunn C.W.*, Rokas A.* 2021. Rooting the animal tree of life. Molecular Biology and Evolution 38: 4322–4333. PDF
23.Li Y., Steenwyk J., Chang Y., Wang Y., James T.Y., Stajich J.E., Spatafora J.W., Groenewald M., Dunn C., Hittinger C.T., Shen X.-X.*, Rokas A.* 2021. A genome-scale phylogeny of the kingdom Fungi. Current Biology 31: 1653-1665. , PDF, Download phylogenomic datagenome data Cover article
22. Novitsky V., Steingrimsson J., Howison M., Dunn C., Gillani, F.S. Manne, A., Li Y., Spence M. Parillo, Z., Fulton J. and Marak T., 2021. Longitudinal typing of molecular HIV clusters in a statewide epidemic. AIDS 35(11):1711-1722. PDF
21. Steenwyk, J. L., M. E. Mead, P. A. Castro, C. Valero, A. Damasio, R. A. C. Santos, A. L. LaBella, Y. Li, S. L. Knowles, H. A. Raja, N. H. Oberlies, X. Zhou, O. A. Cornely, F. Fuchs, P. Koehler*, G. H. Goldman*, & A. Rokas*, 2021. Genomic and phenotypic analysis of COVID-19-associated pulmonary aspergillosis isolates of Aspergillus fumigatus. Microbiology Spectrum 9(1): e00010-21. PDF
20. Steenwyk J., Buida III T.J., LaBella A.L., Li Y., Shen X.-X., Rokas A. 2021. PhyKIT: a UNIX shell toolkit for processing and analyzing phylogenomic data. Bioinformatics 37(16):2325-2331. PDF Download PhyKIT
2020
19. Shen X.-X.*, Li Y., Hittinger C., Chen X., Rokas A.* 2020. An investigation of irreproducibility in maximum likelihood phylogenetic inference. Nature Communications 11:6096. PDF Download data
18. Steenwyk J., Buida III T.J., Li Y., Shen X.-X., Rokas A. 2020. ClipKIT: a multiple sequence alignment-trimming algorithm for accurate phylogenomic inference. PLoS Biology 18: e3001007. PDF Download ClipKT
17. Li Y.#, David K.T.#, Shen X.-X., Steenwyk J., Halanych K.M., Rokas A. 2020. Feature Frequency Profile-based phylogenies are inaccurate. Proc. Natl. Acad. Sci. USA in press. PDF
16. Shen X.-X.*, Steenwyk J., LaBella A., Opulente D., Zhou X., Kominek J., Li Y., Groenewald M., Hittinger C., Rokas A.* 2020. Genome-scale phylogeny and contrasting modes of genome evolution in the fungal phylum Ascomycota. Science Advances 6(45):eabd0079. PDF Download phylogenomic data genome assemblies and annotations
15. Novitsky V., Steingrimsson J.A., Howison M., Gillani F.S., Li Y., Manne A., Fulton J., Spence M., Parillo Z., Marak T. and Chan P.A., 2020. Empirical comparison of analytical approaches for identifying molecular HIV-1 clusters. Scientific Reports 10(1):1-11. PDF
14. Kantor R., Fulton J.P., Steingrimsson J., Novitsky V., Howison M., Gillani F., Li Y., Manne A., Parillo Z., Spence M. and Marak T., 2020. Challenges in evaluating the use of viral sequence data to identify HIV transmission networks for public health. Statistical Communications in Infectious Diseases 12(S1). PDF
13. Kong L.#, Li Y.#, Kocot K.M., Yang Y., Qi L., Li Q. and Halanych K.M.*, 2020. Mitogenomics reveals phylogenetic relationships of Arcoida (Mollusca, Bivalvia) and multiple independent expansions and contractions in mitochondrial genome size. Molecular Phylogenetics and Evolution 150, p.106857. PDF
12. Zhou Y.*, Li Y., Cheng H., Halanych K.M. and Wang C.*, 2020. The mitochondrial genome of the bone-eating worm Osedax rubiplumus (Annelida, Siboglinidae). Mitochondrial DNA Part B 5(3):2267-2268. PDF
11. Zhou Y., Wang, Y. Li, Y., Shen C., Liu Z. and Wang C., 2020. First report of Osedax in the Indian Ocean indicative of trans-oceanic dispersal through the Southern Ocean. Marine Biodiversity 50(1):1-9. PDF
10. Li Y., Tassia M.G., Waits D.S., Bogantes V.E., David K.T. and Halanych K.M., 2019. Genomic adaptations to chemosymbiosis in the deep-sea seep-dwelling tubeworm Lamellibrachia luymesi. BMC Biology 17(1):1-14. PDF
9. Voight J.R., Marshall B.A., Judge J., Halanych K.M., Li Y., Bernardino A.F., Grewe F. and Maddox J.D., 2019. Life in wood: preliminary phylogeny of deep-sea wood-boring bivalves (Xylophagaidae), with descriptions of three new genera and one new species. Journal of Molluscan Studies 85(2):1-9. PDF
8. Li Y.*, Kocot K.M., Tassia M.G., Cannon J.T., Bernt M. and Halanych K.M.*, 2019. Mitogenomics reveals a novel genetic code in Hemichordata. Genome Biology and Evolution 11(1):29-409. PDF
7. Galaska M.P., Li Y., Kocot K.M., Mahon A.R. and Halanych K.M.*, 2019. Conservation of mitochondrial genome arrangements in brittle stars (Echinodermata, Ophiuroidea). Molecular Phylogenetics and Evoluion 30, pp.115-120. PDF
6. Li N., Bao L., Zhou T., Yuan Z., Liu S., Dunham R., Li Y., Wang K., Xu X., Jin Y. and Zeng Q., 2018. Genome sequence of walking catfish (Clarias batrachus) provides insights into terrestrial adaptation. Proc. Natl. Acad. Sci. USA 19(1):1-16. PDF
5. Li Y.*, Liles M.R. and Halanych K.M.*, 2018. Endosymbiont genomes yield clues of tubeworm success. The ISME journal 12(11):2785-2795. PDF
4. Bernardino A.F., Li, Y., Smith C.R. and Halanych K.M., 2017. Multiple introns in a deep-sea Annelid (Decemunciger: Ampharetidae) mitochondrial genome. Scientific Reports 7(1):1-8. PDF
3. Li Y.*, Kocot K.M., Whelan N.V., Santos S.R., Waits D.S., Thornhill D.J. and Halanych K.M.*, 2017. Phylogenomics of tubeworms (Siboglinidae, Annelida) and comparative performance of different reconstruction methods. Zoologica Scripta 46(2):200-213. PDF
2. Waits D.S., Santos S.R., Thornhill D.J., Li Y. and Halanych K.M.*, 2016. Evolution of sulfur binding by hemoglobin in Siboglinidae (Annelida) with special reference to bone-eating worms, Osedax. Journal of molecular evolution 82(4-5):219-229. PDF
1. Li Y., Kocot K.M., Schander C., Santos S.R., Thornhill D.J. and Halanych K.M., 2015. Mitogenomics reveals phylogeny and repeated motifs in control regions of the deep-sea family Siboglinidae (Annelida). Molecular Phylogenetics and Evolution 85:221-229. PDF
