Research articles

2024

50. Liu C.#, Zhou X.#, Li Y., Hittinger C., Pan R., Huang J.-Y., Chen X., Rokas A., Chen Y., Shen X.-X.* 2024. The influence of the number of tree searches on maximum likelihood inference in phylogenomics. Systematic Biology 73(5):807-822. PDF Download data

49. Tao M.#, Chen J.#, Cui C.#, Xu Y#, Xu J., Shi Z., Yun J., Zhang J., Ou G., Liu C., Chen Y., Zhu Z., Pan R., Xu S., Chen X., Rokas A., Zhao Y., Wang S.*, Huang J.*, Shen X.-X.* 2024. Identification of a longevity gene through evolutionary rate covariation of insect mito-nuclear genomes. Nature Aging 4(8):1076–1088. PDF Download data

48. Opulente D.A., LaBella A.L., Harrison M.-C., Wolters J.F., Liu C.,Li Y., Kominek J., Steenwyk J.L., Stoneman H.R., VanDenAvond J., Miller C.R., Langdon Q.K., Silva M., Gonçalves C., Ubbelohde E.J., Li Y., Buh K. V., Jarzyna M., Haase M.A.B., Rosa C.A., ČCadež N., Libkind D., DeVirgilio J.H., Hulfachor A.B., Kurtzman C.P., Sampaio J.P., Gonçalves P., Zhou X., Shen X.-X., Groenewald M., Rokas A., Hittinger C.T. 2024. Genomic factors shape carbon and nitrogen metabolic niche breadth across Saccharomycotina yeasts. Science (80-. ). 384. PDF

47. David K.T., Harrison M.-C., Opulente D.A., LaBella A.L., Wolters J.F., Zhou X., Shen X.-X., Groenewald M., Pennell M., Hittinger C.T., Rokas A. 2024. Saccharomycotina yeasts defy long-standing macroecological patterns. Proc. Natl. Acad. Sci. USA 121 (10) e2316031121. PDF

46. Harrison M.-C., Ubbelohde E.J., LaBella A.L., Opulente D.A., Wolters J.F., Zhou X., Shen X.-X., Groenewald M., Hittinger C.T., Rokas A. 2024. Machine learning enables identification of an alternative yeast galactose utilization pathway. Proc. Natl. Acad. Sci. USA 121 (18) e2315314121. PDF

2023

45. Liu C., Han X., Steenwyk J.L., Shen X.-X.* 2023. Temporal transcriptomics provides insights into host‒pathogen interactions: a case study of Didymella pinodella and disease-resistant and disease-susceptible pea varieties. Crop Health 1:5 PDF

44. Steenwyk J.L., Li Y., Zhou X., Shen X.-X., Shen X.-X., Rokas A.* 2023. Incongruence in the phylogenomics era. Nature Reviews Genetics 24:834–850 PDF

43. Chen S.-J., Zhang J.-L., Ma W.-J., Wu H.-J., Li Y., Shen X.-X., Xu H.-J.* 2023. FoxO and rotund form a binding complex governing wing polyphenism in planthoppers. iScience 26:107182. PDF

42. Groenewald M.*, Hittinger C.T., Bensch K., Opulente D.A., Shen X.-X., Li Y., Liu C., LaBella A.L., Zhou X., Limtong S., Jindamorakot S., Gonçalves P., Robert V., Wolfe K.H., Rosa C.A., Boekhout T., Ĉadež N., Péter G., Sampaio J.P., Lachance M.-A., Yurkov A.M., Daniel H.-M., Takashima M., Boundy-Mills K., Libkind D., Aoki K., Sugita T., Rokas A. 2023. A genome-informed higher rank classification of the biotechnologically important fungal subphylum Saccharomycotina. Studies in Mycology 105:1-22. PDF

41. Liu C., Li Y., Chen Y., Chen X.-X., Huang J., Rokas A., Shen X.-X.* 2023. How has horizontal gene transfer shaped the evolution of insect genomes? Environmental Microbiology 25(3):642–645. PDF

2022

40. Li Y.-N.*, Liu H., Steenwyk J.L., LaBella A.L., Harrison M.-C., Groenewald M., Zhou X., Shen X.-X., Zhao T., Hittinger C.T., Rokas A.* 2022. Contrasting modes of macro and microsynteny evolution in a eukaryotic subphylum. Current Biology 32(24):5335-5343. PDF

39. Steenwyk, J.L.*, Goltz, D.C., Buida, T.J., Li, Y., Shen X.-X., and Rokas, A.* 2022. OrthoSNAP: A tree splitting and pruning algorithm for retrieving single-copy orthologs from gene family trees. PLoS biology 20(10):e3001827. PDF

38. Ma, X.-Z., Wang, Z.-Q., Ye, X.-Q., Liu, X.-Y., Tang, P., Shen X.-X., and Chen, X.-X.* 2022. A high-quality genome of the dobsonfly Neoneuromus ignobilis reveals molecular convergences in aquatic insects. Genomics 114(5):110437. PDF

37. Li Y.#, Liu Z.#, Liu C.#, Shi Z., Pang L., Chen C., Chen Y., Pan R., Zhou W., Chen X.-X., Rokas A.*, Huang J.*, Shen X.-X.* 2022. HGT is widespread in insects and contributes to male courtship in lepidopterans. Cell 185(16):2975-2987. PDF Download data and additional figures & tables, HGTfinder

36. Deng Q.#, Li H.#, Feng Y.#, Xu R., Li W., Zhu R., Akhter D., Shen X.-X., Hu J.*, Jiang H.*, Pan R.* 2022. Defining upstream enhancing and inhibiting sequence patterns for plant peroxisome targeting signal type 1 using large‐scale in silico and in vivo analyses. The Plant Journal 111(2):567-582. PDF

35. Xu S.#, Liu Y.-X.#, Cernava T.#, Wang H., Zhou Y., Xia T., Cao S., Berg G., Shen X.-X., Wen Z., Li C., Qu B., Ruan H., Chai Y., Zhou X., Ma Z., Shi Y., Yu Y.*, Bai Y.*, Chen Y.* 2022. Fusarium fruiting body microbiome member Pantoea agglomerans inhibits fungal pathogenesis by targeting lipid rafts. Nature microbiology 7(6): 831-843. PDF

2021

34. Phillips, M. A., Steenwyk J.*, Shen X.-X., Rokas A.* 2021. Examination of gene loss in the DNA mismatch repair pathway and its mutational consequences in a fungal phylum. Genome Biology and Evolution 13(10):1-12. PDF

33. Tice, A. K.#, D. Žihala#, T. Pánek#, R. E. Jones, E. Salomaki, S. Nenarokov, F. Burki, M. Eliáš, L. Eme, A. J. Roger, A. Rokas, Shen X.-X., J. F. H. Strassert, M. Kolísko, M. W. Brown* 2021. PhyloFisher: A phylogenomic package for resolving eukaryotic relationships. PLoS Biology 19: e3001365. PDF Download PhyloFisher.

32. Li Y., Shen X.-X., Evans B., Dunn C.W.*, Rokas A.* 2021. Rooting the animal tree of life. Molecular Biology and Evolution 38(10):4322-4333. PDF

31. Shen X.-X.*, Steenwyk J., Rokas A. 2021. Dissecting incongruence between concatenation- and quartet-based approaches in phylogenomic data. Systematic Biology 70(5):997-1014. PDF Download data GLS&GQS caculation

30. 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 data, genome data.

29. 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

28. 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.

27. 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.

26. Haase M.A.B.#, Kominek J.#, Opulente D., Shen X.-X., LaBella A., Zhou X., DeVirgilio J., Hulfachor A, Kurtzman C.P., Rokas A.*, Hittinger C.T.* 2020. Repeated horizontal gene transfer of GALactose metabolism genes violates Dollo’s law of irreversible loss. Genetics 217: iyaa012. PDF

25. Li Y.#, Davod 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 117(50):31580-31581. PDF

24. 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.

23. Mead M.#, Borowsky A.#, Joehnk B., Steenwyk J., Shen X.-X., Sil A., Rokas A.* 2020. Recurrent loss of abaA, a master regulator of asexual development in filamentous fungi, correlates with changes in genomic and morphological traits. Genome Biology and Evolution 12(7):1119–1130. PDF

22. Yang Y., Sun P., Lv L., Wang D., Ru D., Li Y., Ma T., Zhang L., Shen X.-X., Meng F., Jiao B., Shan L., Liu M., Wang Q., Qin Z., Xi Z., Wang X., Davis C.C., Liu J.* 2020. Prickly waterlily and rigid hornwort genomes shed light on early angiosperm evolution. Nature Plants 6(3):215–222. PDF
Commentary in Nature Plants

Before 2020

21. Ely Z.A., Moon J.M., Sliwoski G.R., Sangha A.K., Shen X.-X., Labella A.L., Meiler J., Capra J.A., Rokas A.* 2019. The impact of natural selection on the evolution and function of placentally expressed galectins. Genome Biology and Evolution 11(9):2574–2592 PDF

20. Krassowski, T., J. Kominek, Shen X.-X., D. A. Opulente, X. Zhou, A. Rokas, C. T. Hittinger, Wolfe K.H.* 2019. Multiple Reinventions of Mating-type Switching during Budding Yeast Evolution. Current Biology 29(15):2555–2562. PDF
Commentary in Current Biology

19. Wang M., Fu H., Shen X.-X., Ruan R., Rokas A., Li H.* 2019. Genomic features and evolution of the conditionally dispensable chromosome in the tangerine pathotype of Alternaria and alternata. Mol. Plant Pathol. 20(10): 1425–1438. PDF

18. Steenwyk, J. L., Shen X.-X., A. L. Lind, G. G. Goldman, Rokas A. 2019.* A robust phylogenomic timetree for biotechnologically and medically important fungi in the genera Aspergillus and Penicillium. mBio 10: 1-25. PDF

17. Steenwyk, J. L., D. A. Opulente, J. Kominek, Shen X.-X., X. Zhou, A. L. Labella, N. P. Bradley, B. F. Eichman, N. Čadež, D. Libkind, J. DeVirgilio, A. B. Hulfachor, Kurtzman C.P., Hittinger C.T., Rokas A.* 2019. Extensive loss of cell cycle and DNA repair genes in an ancient lineage of bipolar budding yeasts. PLoS Biology 17: e3000255. PDF

16. Kominek J.#, Doering D.T.#, Opulente D., Shen X.-X., Zhou X., Jeremy D., Hulfachor A.B., Groenewald M., Mcgee M., Karlen S., Kurtzman C.P., Rokas A., Hittinger C.T.* 2019. Eukaryotic acquisition of a bacterial operon. Cell 176: 1356-1366. PDF

Commentary in Cell

15. Shen X.-X.#, Opulente D.A.#, Kominek J.#, Zhou X.#, Steenwyk J., Buh K.V., Haase M., Wisecaver J.H., Wang M., Doering D.T., Boudouris J., Schneider R., Langdon Q.K., Ohkuma M., Endoh R., Takashima M., Manabe R., Čadež N., Libkind D., Rosa C., DeVirgilio J., Hulfachor A., Groenewald M., Kurtzman C.P., Hittinger C.T.*, Rokas A.* 2018. The tempo and mode of genome evolution in the budding yeast subphylum. Cell 175: 1533-1545. PDF Download data

Featured article on the homepage of the US Department of Energy Office of Science on December 4 2018
The story behind the paper in Nature Ecology & Evolution blog

14. Krause D.J., Kominek J., Opulente D.A., Shen X.-X., Zhou X., Langdon Q.K., DeVirgilio J., Hulfachor A., Kurtzman C.P., Rokas A., Hittinger C.T.* 2018. Functional and evolutionary characterization of a secondary metabolite gene cluster in budding yeasts. Proc. Natl. Acad. Sci. USA 115: 11030-11035. PDF

13. Shi R., Shen X.-X., Rokas A., Eichman B.F.* 2018. Structural biology of the HEAT-like repeat family of DNA glycosylases. BioEssays 40: 1800133. PDF

12. Krassowski T., Coughlan A.Y., Shen X.-X., Zhou X., Kominek J., Opulente D.A., Riley R., Grigoriev I. V., Maheshwari N., Shields D.C., Kurtzman C.P., Hittinger C.T., Rokas A., Wolfe K.H.* 2018. Evolutionary instability of CUG-Leu in the genetic code of budding yeasts. Nature Communications 9: 1887. PDF

11. Gonçalves C., Wisecaver J.H., Kominek J., Oom M.S., Leandro M.J., Shen X.-X., Opulente D.A., Zhou X., Peris D., Kurtzman C.P., Hittinger C.T., Rokas A., Gonçalves P.* 2018. Evidence for loss and adaptive reacquisition of alcoholic fermentation in an early-derived fructophilic yeast lineage. eLife 7: e33034. PDF

10. Zhou X., Shen X.-X., Hittinger C.T., Rokas A.* 2018. Evaluating Fast Maximum Likelihood-Based Phylogenetic Programs Using Empirical Phylogenomic Data Sets. Molecular Biology and Evolution 35(2): 486-503. PDF Download data

9. Shi R., Mullins E.A., Shen X.-X., Lay K.T., Yuen P.K., David S.S., Rokas A., Eichman B.F.* 2018. Selective base excision repair of DNA damage by the non-base-flipping DNA glycosylase AlkC. EMBO Journal 37: 63-74. PDF

8. Shen X.-X., Hittinger C. T., Rokas A.* 2017. Contentious relationships in phylogenomic studies can be driven by a handful of genes. Nature Ecology and Evolution 1: 0126. PDF Download data Phylogenetic signal parser v1.1

One of 12 evolutionary biological papers in 2017 and 2018 (Nature Ecol & Evol's 2nd Anniversary)
One of 10 editors’ and readers’ favourites in 2017 (Nature Ecol & Evol's 1st Anniversary)
The story behind the paper in Nature Ecology & Evolution blog

7. Shen X.-X., Zhou X., Kominek J., Kurtzman C. P., Hittinger C. T., Rokas A.* 2016. Reconstructing the backbone of the Saccharomycotina yeast phylogeny using genome-scale data. G3: Genes | Genomes | Genetics 6: 3927-3939. PDF Download data
One of the most cited papers in G3 (G3 10th Anniversary)

6. Shen X.-X., Salichos L., Rokas A.* 2016. A genome-scale investigation of how sequence-, function-, and tree-based gene properties influence phylogenetic inference. Genome Biology and Evolution 8(8): 2565–2580. PDF Download data

5. Shen X.-X., Liang D., Chen M.Y., Mao R.L., Wake D.B., Zhang P.* 2016. Enlarged Multilocus Dataset Provides Surprisingly Younger Time of Origin for the Plethodontidae, the Largest Family of Salamanders. Systematic Biology 65(1): 66-81. PDF Download data

4. Shen X.-X., Liang D., Feng Y.J., Chen M.Y., Zhang P.* 2013. A Versatile and Highly Efficient Toolkit Including 102 Nuclear Markers for Vertebrate Phylogenomics, Tested by Resolving the Higher-level Relationships of the Caudata. Molecular Biology and Evolution 30(10): 2235-2248. PDF Download data

3. Liang D.#, Shen X.-X.#, Zhang P.* 2013. One Thousand Two Hundred Ninety Nuclear Genes from a Genome-Wide Survey Support Lungfishes as the Sister Group of Tetrapods. Molecular Biology and Evolution 30(8): 1803-1807. PDF Download data

2. Shen X.-X.#, Liang D.#, Zhang P.* 2012. The Development of Three Long Universal Nuclear Protein-Coding Locus Markers and Their Application to Osteichthyan Phylogenetics with Nested PCR. PLoS ONE 7(6): e39256.62. PDF Download data

1. Shen X.-X., Liang D, Wen J.Z., Zhang P.* 2011. Multiple Genome Alignments Facilitate Development of NPCL Markers: A Case Study of Tetrapod Phylogeny Focusing on the Position of Turtles. Molecular Biology and Evolution 28(12): 3237-3252. PDF Download data