publications

— 2024 —

Chen, G., Yu, D., Yang, Y., …  Feng, S.* (2024). Adaptive expansion of ERVK solo-LTRs is associated with Passeriformes speciation events. Nature Communications, 15, 3151 .

Stiller, J., Feng, S., Chowdhury, A. A., Rivas-González, I., Duchêne, D. A., Fang, Q., … & Zhang, G.* (2024). Complexity of avian evolution revealed by family-level genomes. Nature, 1-3.

— 2023 —

Wanders, K., Chen, G., Feng, S., Zhang, G., Székely, T., Bruford, M., … Urrutia, A.* (2023). Polygamy and purifying selection in birds. Evolution, 77(1), 276-288.

Germain, R. R., Feng, S., Buffan, L., Carmona, C. P., Chen, G., Graves, G. R., … Nogués-Bravo, D.* (2023). Changes in the functional diversity of modern bird species over the last million years. Proceedings of the National Academy of Sciences, 120(7), e2201945119.

Germain, R. R., Feng, S., Chen, G., Graves, G. R., Tobias, J. A., Rahbek, C., … Zhang, G.* & Nogués-Bravo, D.* (2023). Species-specific traits mediate avian demographic responses under past climate change. Nature Ecology & Evolution, 1-11.

Bi, X., Zhou, L., Zhang, J. J., Feng, S., Hu, M., Cooper, D. N., … Wu, D.* & Zhang, G.* (2023). Lineage-specific accelerated sequences underlying primate evolution. Science Advances, 9(22), eadc9507.

— 2022 —

Femerling, G., Van Oosterhout, C., Feng, S., Bristol, R., Zhang, G., Groombridge, J., … Morales, H. E.* (2022). Genetic load and adaptive potential of a recovered avian species that narrowly avoided extinction. bioRxiv, 20.521169.

Feng, S.#, Bai, M.#, Rivas-González, I., Li, C., Liu, S., Tong, Y., Yang, H., Chen, G., Xie, D., Sears, K. E., Franco, L. M., Gaitan-Espitia, J. D., Nespolo, R. F., Johnson, W. E., Yang, H., Brandies, P. A., Hogg, C. J., Belov, K., Renfree, M. B., … Zhang, G.* (2022). Incomplete lineage sorting and phenotypic evolution in marsupials. Cell, 185(10): 1646-1660.e18.

Ji, Y., Feng, S., Wu, L., Fang, Q., Brüniche-Olsen, A., DeWoody, J.A., Cheng, Y., Zhang, D., Hao, Y., Song, G., Qu, Y., Suh, A., Zhang, G.*, Hackett, S.J.*, & Lei, F.*  (2022). Orthologous microsatellites, transposable elements, and DNA deletions correlate with generation time and body mass in neoavian birds. Science Advances 8, eabo0099.

Wang, Z.#, Zhang, J.#, Xu, X., Witt, C., Deng, Y., Chen, G., Meng, G., Feng, S., Xu, L., Szekely, T., Zhang, G.*, & Zhou, Q.* (2022). Phylogeny and sex chromosome evolution of Palaeognathae. Journal of Genetics and Genomics, 49(2), 109-119. [cover story]

Li, X.#, Gao, R.#, Chen, G., Price, A. L., Øksnebjerg, D. B., Hosner, P. A., Zhou, Y., Zhang, G., & Feng, S.* (2022). Draft genome assemblies of four manakins. Scientific Data, 9(1), 564.

Cole, T.L.*#, Zhou, C.#, Fang, M.#, Pan, H., Ksepka, D.T., Fiddaman, S.R., Emerling, C.A., Thomas, D.B., Bi, X., Fang, Q., Ellegaard, M.R., Feng, S., … Zhang, G.* (2022). Genomic insights into the secondary aquatic transition of penguins. Nature Communications, 13, 3912.

— 2021 —

Xie, D.*, Chen, G., Meng, X., Wang, H., Bi, X., Fang, M., Yang, C., Zhou, Y., Long, E., & Feng, S.* (2021). Comparable Number of Genes Having Experienced Positive Selection among Great Ape Species. Animals, 11(11), 3264.

Liu, J.#, Wang, Z.#, Li, J., Xu, L., Liu, J., Feng, S., Guo, C., Chen, S., Ren, Z., Rao, J., Wei, K., Chen, Y., Jarvis, E. D., Zhang, G., & Zhou, Q.* (2021). A new emu genome illuminates the evolution of genome configuration and nuclear architecture of avian chromosomes. Genome Research, 31(3), 497–511.

Li, J., Zhang, J., Liu, J., Zhou, Y., Cai, C., Xu, L., Dai, X., Feng, S., Guo, C., Rao, J., Wei, K., Jarvis, E. D., Jiang, Y., Zhou, Z., Zhang, G., & Zhou, Q.* (2021). A new duck genome reveals conserved and convergently evolved chromosome architectures of birds and mammals. GigaScience, 10(1), giaa142.

Thorup, K.*, Pedersen, L., da Fonseca, R. R., Naimi, B., Nogués-Bravo, D., Krapp, M., Manica, A., Willemoes, M., Sjöberg, S., Feng, S., Chen, G., Rey-Iglesia, A., Campos, P. F., Beyer, R., Araújo, M. B., Hansen, A. J., Zhang, G., Tøttrup, A. P., & Rahbek, C. (2021). Response of an Afro-Palearctic bird migrant to glaciation cycles. Proceedings of the National Academy of Sciences, 118(52).

Sinding, M.-H. S.,#* Ciucani, M. M.#, Ramos-Madrigal, J.#, Carmagnini, A., Rasmussen, J. A., Feng, S., Chen, G., Vieira, F. G., Mattiangeli, V., Ganjoo, R. K., Larson, G., Sicheritz-Pontén, T., Petersen, B., Frantz, L., Gilbert, M. T. P., & Bradley, D. G. (2021). Kouprey (Bos sauveli) genomes unveil polytomic origin of wild Asian Bos. iScience, 24(11), 103226.

Wang, M.#, Zhang, J.#, Guo, X.#, Li, M.#, Meyer, R.#, Ashari, H.#, Zheng, Z., Wang, S., Peng, M., Jiang, Y., Thakur, M., Suwannapoom, C., Esmailizadeh, A., Hirimuthugoda, N. Y., Zein, M. S. A., Kusza, S., Kharrati-Koopaee, H., Zeng, L., Wang, Y., …, Feng, S., …, Zhang, Y.* (2021). Large-scale genomic analysis reveals the genetic cost of chicken domestication. BMC Biology, 19(1), 118.

Pietri, V. L. D.*, De Pietri, V. L., Worthy, T. H., Paul Scofield, R., Cole, T. L., Wood, J. R., Mitchell, K. J., Cibois, A., Jansen, J. J. F., Cooper, A. J., Feng, S., Chen, W., Tennyson, A. J., & Wragg, G. M. (2021). A new extinct species of Polynesian sandpiper (Charadriiformes: Scolopacidae: Prosobonia) from Henderson Island, Pitcairn Group, and the phylogenetic relationships of Prosobonia. Zoological Journal of the Linnean Society, 192(4), 1045–1070.

Wang Z., Chen G., Zhang G.*, Zhou Q.* (2021). Dynamic evolution of transposable elements, demographic history, and gene content of paleognathous birds. Zoological Research, 42(1): 51-61.

— 2020 —

Feng, S.#, Stiller, J.#, Deng, Y.#, Armstrong, J.#, Fang, Q., Reeve, A. H., Xie, D., Chen, G., Guo, C., Faircloth, B. C., Petersen, B., Wang, Z., Zhou, Q., Diekhans, M., Chen, W., Andreu-Sánchez, S., Margaryan, A., Howard, J. T., Parent, C., … Zhang, G.* (2020). Dense sampling of bird diversity increases power of comparative genomics. Nature, 587(7833), 252–257. [cover story]

Armstrong, J., Hickey, G., Diekhans, M., Fiddes, I. T., Novak, A. M., Deran, A., Fang, Q., Xie, D., Feng, S., Stiller, J., Genereux, D., Johnson, J., Marinescu, V. D., Alföldi, J., Harris, R. S., Lindblad-Toh, K., Haussler, D., Karlsson, E., Jarvis, E. D., … Paten, B.* (2020). Progressive Cactus is a multiple-genome aligner for the thousand-genome era. Nature, 587(7833), 246–251. [cover story]

Gelabert, P., Sandoval-Velasco, M., Serres, A., de Manuel, M., Renom, P., Margaryan, A., Stiller, J., de-Dios, T., Fang, Q., Feng, S., Mañosa, S., Pacheco, G., Ferrando-Bernal, M., Shi, G., Hao, F., Chen, X., Petersen, B., Olsen, R-A., Navarro, A., … Lalueza-Fox, C.* (2020). Evolutionary History, Genomic Adaptation to Toxic Diet, and Extinction of the Carolina Parakeet. Current Biology, 30(1), 108-114.

Wang, M.#, Thakur, M.#, Peng, M.#, Jiang, Y.#, Frantz, L. A. F.#, Li, M.#, Zhang, J., Wang, S., Peters, J., Otecko, N. O., Suwannapoom, C., Guo, X., Zheng, Z., Esmailizadeh, A., Hirimuthugoda, N. Y., Ashari, H., Suladari, S., Zein, M. S. A., Kusza, S., …, Feng, S., …, Zhang, Y.* (2020). 863 genomes reveal the origin and domestication of chicken. Cell Research, 30(8), 693–701.

— 2019 —

Feng, S., Fang, Q., Barnett, R., Li, C., Han, S., Kuhlwilm, M., Zhou, L., Pan, H., Deng, Y., Chen, G., Gamauf, A., Woog, F., Prys-Jones, R., Marques-Bonet, T., Gilbert, M. T. P., & Zhang, G.* (2019). The Genomic Footprints of the Fall and Recovery of the Crested Ibis. Current Biology, 29(2), 340–349.e7.

Xu, L., Auer, G., Peona, V., Suh, A., Deng, Y., Feng, S., Zhang, G., Blom, M. P. K., Christidis, L., Prost, S., Irestedt, M., & Zhou, Q. (2019). Dynamic evolutionary history and gene content of sex chromosomes across diverse songbirds. Nature Ecology & Evolution, 3(5), 834.

— 2018 —

Kukekova, A. V.#, Johnson, J. L., Xiang, X., Feng, S., Liu, S., Rando, H. M., Kharlamova, A. V., Herbeck, Y., Serdyukova, N. A., Xiong, Z., Beklemischeva, V., Koepfli, K.-P., Gulevich, R. G., Vladimirova, A. V., Hekman, J. P., Perelman, P. L., Graphodatsky, A. S., O’Brien, S. J., Wang, X., … Zhang, G.# (2018). Red fox genome assembly identifies genomic regions associated with tame and aggressive behaviours. Nature Ecology & Evolution, 2(9),1479–1491.

Rando, H., Farré, M., Robson, M., Won, N., Johnson, J., Buch, R., Bastounes, E., Xiang, X., Feng, S., Liu, S., Xiong, Z., Kim, J., Zhang, G., Trut, L., Larkin, D., & Kukekova, A.# (2018). Construction of Red Fox Chromosomal Fragments from the Short-Read Genome Assembly. Genes, 9(6): 308.