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04 / 07 / 2023
The article“Evolution of sexualsystems, sex chromosomes andsex-linked gene transcription inflatworms and roundworms" madit into the Top 25 NatureCommunications life andbiological sciences articles of 2022.
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06 / 01 / 2023
Biggest ever study of primate genomes has surprises for humanity
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06 / 01 / 2023
Hundreds of new primate genomes offer window into human health—and our past
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J. Wu, Q. Deng, Y. Qiu, C. Liu, C. Lin, Y. Ru, et al. Post-transfer adaptation of HGT-acquired genes and contribution to guanine metabolic diversification in land plants.
New Phytologist
(2024)
X. Zhang, Xie, N., Ding, G., Ning, D., Dai, W., Xiong, Z., et al. An evolutionarily conserved pathway mediated by neuroparsin-A regulates reproductive plasticity in ants.
PLOS Biology
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K. Wu, D. Qin, Y. Qian, H. Liu. A new era of mutation rate analyses : Concepts and methods.
Zoological Research
(2024)
W. Weng, Y. Deng, R. Deviatiiarov, S. Hamidi, E. Kajikawa, O. Gusev, et al. ETV2 induces endothelial, but not hematopoietic, lineage specification in birds.
Life Science Alliance
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D.A. Opulente, A.L. LaBella, M.C. Harrison, J.F. Wolters, C. Liu, Y. Li, et al. Genomic factors shape carbon and nitrogen metabolic niche breadth across Saccharomycotina yeasts.
Science
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Z. Jiang, W. Zang, P.G.P. Ericson, G. Song, S. Wu, S. Feng, et al. Gene flow and an anomaly zone complicate phylogenomic inference in a rapidly radiated avian family (Prunellidae).
BMC Biology
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L. Sun, K.T. David, J.F. Wolters, S.D. Karlen, C. Gonçalves, D.A. Opulente, et al. Functional and Evolutionary Integration of a Fungal Gene With a Bacterial Operon.
Molecular Biology and Evolution
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Z. Zhu, L. Younas, Q. Zhou. Evolution and regulation of animal sex chromosomes.
Nature Reviews Genetics
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C. Liu, X. Zhou, Y. Li, C. T. Hittinger, R. Pan, J. Huang, et al. The influence of the number of tree searches on maximum likelihood inference in phylogenomics.
Systematic Biology
(2024)
M. Tao, J. Chen, C. Cui, Y. Xu, J. Xu, Z. Shi, et al. Identification of a longevity gene through evolutionary rate covariation of insect mito-nuclear genomes.
Nature Aging
(2024)
K. Wanders, G. Chen, S. Feng, T. Székely, A.O. Urrutia. Role-reversed polyandry is associated with faster fast-Z in shorebirds.
Proceedings B
(2024)
G. Chen, D. Yu, Y. Yang, X. Li, X. Wang, D. Sun, et al. Adaptive expansion of ERVK solo-LTRs is associated with Passeriformes speciation events.
Nature communication
(2024)
J. Stiller, S. Feng, A.-A. Chowdhury, I. Rivas-González, D. A. Duchêne, Q. Fang, et al. Complexity of avian evolution revealed by family-level genomes.
Nature
(2024)
S. Mirarab, I. Rivas-González, S. Feng, J. Stiller, Q. Fang, U. Mai, et al. A region of suppressed recombination misleads neoavian phylogenomics.
Proceedings of the National Academy of Sciences
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Y Xie and G Zhang. Phylogenomic analyses unraveled the evolution of viral tolerance in bats.
Cell Genomics
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S. Mirarab, I. Rivas-González, S. Feng, J. Stiller, Q. Fang, U. Mai, et al. A region of suppressed recombination misleads neoavian phylogenomics.
Proceedings of the National Academy of Sciences
121, e2319506121. (2024)
J. Stiller, S. Feng, A.-A. Chowdhury, I. Rivas-González, D. A. Duchêne, Q. Fang, et al. Complexity of avian evolution revealed by family-level genomes.
Nature
(2024)
B. Hu, X. Zhuang, L. Zhou, G. Zhang, D. Cooper, D. Wu. Deciphering the role of rapidly evolving conserved elements in primate brain development and exploring their potential involvement in Alzheimer’s disease.
Mol Biol Evol
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P. A. O'Brien, S. Tan, P. R. Frade, S. J. Robbins, J. P. Engelberts, S. C. Bell, et al. Validation of key sponge symbiont pathways using genome-centric metatranscriptomics.
Environmental Microbiology
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K. Wanders, G. Chen, S. Feng, G. Zhang, T. Székely, M. Bruford, et al. Polygamy and purifying selection in birds.
Evolution
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J. Smith, J. M. Alfieri, N. Anthony, P. Arensburger, G. N. Athrey, J. Balacco, et al. Fourth Report on Chicken Genes and Chromosomes 2022.
Cytogenetic and Genome Research
162, 405-528. (2023)
G. Femerling, C. van Oosterhout, S. Feng, R. M. Bristol, G. Zhang, et al. Genetic Load and Adaptive Potential of a Recovered Avian Species that Narrowly Avoided Extinction.
Mol Biol Evol
40,12 (2023)
L. F. K. Kuderna, J. C. Ulirsch, S. Rashid, M. Ameen, et al. Identification of constrained sequence elements across 239 primate genomes.
Nature
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H. Liu, M. Sun, J. Zhang. Genomic estimates of mutation and substitution rates contradict the evolutionary speed hypothesis of the latitudinal diversity gradient.
Proc. R. Soc. B
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C. Liu, X. Han, J. L. Steenwyk, X.‐X. Shen. Temporal transcriptomics provides insights into host‒pathogen interactions: a case study of Didymella pinodella and disease-resistant and disease-susceptible pea varieties.
Crop Health
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D. Wu, L. Xie, Y. Sun, Y. Huang, L. Jia, C. Dong, et al. A syntelog-based pan-genome provides insights into rice domestication and de-domestication.
Genome Biology
24, 179. (2023)
XL. Zhuang, JJ. Zhang, Y. Shao, Y. Ye, CY. Chen, L. Zhou, et al. Integrative omics reveals rapidly evolving regulatory sequences driving primate brain evolution.
Mol Biol Evol
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C. Yang, Y. Zhou, Y. Song, D. Wu, Y. Zeng, L. Nie, et al. The complete and fully-phased diploid genome of a male Han Chinese.
Cell Res
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H. Gao, T. Hamp, J. Ede, J. G. Schraiber, J. McRae, M. Singer-Berk, et al. The landscape of tolerated genetic variation in humans and primates.
Science
380(6648), eabn8153. (2023)
L. F. K. Kuderna, H. Gao, M. C. Janiak, M. Kuhlwilm, J. D. Orkin, T. Bataillon, et al. A global catalog of whole-genome diversity from 233 primate species.
Science
380(6648), 906-913. (2023)
X.-G. Qi, J. Wu, L. Zhao, L. Wang, X. Guang, P. A. Garber, et al. Adaptations to a cold climate promoted social evolution in Asian colobine primates.
Science
380(6648), eabl8621. (2023)
I. Rivas-González, M. Rousselle, F. Li, L. Zhou, J. Y. Dutheil, K. Munch, et al.Pervasive incomplete lineage sorting illuminates speciation and selection in primates.
Science
380(6648), eabn4409. (2023)
Y. Shao, L. Zhou, F. Li, L. Zhao, B.-L. Zhang, F. Shao, et al. Phylogenomic analyses provide insights into primate evolution.
Science
380(6648), 913-924. (2023)
B.-L. Zhang, W. Chen, Z. Wang, W. Pang, M.-T. Luo, S. Wang, et al. Comparative genomics reveals the hybrid origin of a macaque group.
Sci Adv
9(22), eadd3580. (2023)
X. Bi, L. Zhou, J.-J. Zhang, S. Feng, M. Hu, D. N. Cooper, et al. Lineage-specific accelerated sequences underlying primate evolution.
Sci Adv
9(22), eadc9507. (2023)
Y. Zhou, X. Zhan, J. Jin, L. Zhou, J. Bergman, X. Li, et al. Eighty million years of rapid evolution of the primate Y chromosome.
Nat Ecol Evol
(2023)
R. R. Germain, S. Feng, G. Chen, G. R. Graves, J. A. Tobias,, et al. Species-specific traits mediate avian demographic responses under past climate change.
Nat Ecol Evol
(2023)
Z. Huang, L. Xu, C. Cai, Y. Zhou, J. Liu, Z. Xu, et al. Three amphioxus reference genomes reveal gene and chromosome evolution of chordates.
PNAS
120 (10) e2201504120 (2023)
L. A. Bergeron, S. Besenbacher, J. Zheng, P. Li, M. F. Bertelsen, B. Quintard, et al. Evolution of the germline mutation rate across vertebrates.
Nature
615, 285–291 (2023).
R. R. Germain, S. Feng, L. Buffan, C. P. Carmona, G. Chen, G. R. Graves, et al. Changes in the functional diversity of modern bird species over the last million years.
PNAS
120(7), e2201945119 (2023)
P. Zhang, Y. Zhu, Q. Guo, J. Li, X. Zhan, H. Yu, et al. On the origin and evolution of RNA editing in metazoans.
Cell Rep
42(2), 112 (2023)
K. Wanders, G. Chen, S. Feng, G. Zhang, T. Szekely, M. Bruford, et al. Polygamy and purifying selection in birds.
Evolution
77(1), 276-288 (2023)
G. Zhang. The mutation rate as an evolving trait.
Nat Rev Genet
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X. Long, D. Charlesworth, J. Qi, R. Wu, M. Chen, Z. Wang, et al. Independent Evolution of Sex Chromosomes and Male Pregnancy-Related Genes in Two Seahorse Species.
Mol Biol Evol
40, 1 (2022)
Y. Zhuang, W. Xu, G. Zhang, H. Mai, X. Li, H. He, et al. Unparalleled details of soft tissues in a Cretaceous ant.
BMC Ecol Evo
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C. Liu, Y. Li, Y. Chen, X. X. Chen, J. Huang, A. Rokas, et al. How has horizontal gene transfer shaped the evolution of insect genomes?
Environ Microbiol
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E. D. Jarvis, G. Formenti, A. Rhie, A. Guarracino, C. Yang, J. Wood, et al. Semi-automated assembly of high-quality diploid human reference genomes.
Nature
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Q.Zhou. A chromosome minimalist view of genome regulation and evolution based on mouse chromosome engineering.
Zool Res
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B. Qiu, X. Dai, P. Li, R. S. Larsen, R. Li, A. L. Price, et al. Canalized gene expression during development mediates caste differentiation in ants.
Nat Ecol Evol
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X Li, R Gao, G Chen, A. L. Price, D. B.i Øksnebjerg, P. A. Hosner, Y Zhou, G Zhang & S Feng. Draft genome assemblies of four manakins.
Sci Data
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Y. Ji, S. Feng, L. Wu, Q. Fang, A. Bruniche-Olsen, J. A. DeWoody, et al. Orthologous microsatellites, transposable elements, and DNA deletions correlate with generation time and body mass in neoavian birds.
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L. Ferrandez-Peral, X. Zhan, M. Alvarez-Estape, C. Chiva, P. Esteller-Cucala, R. Garcia-Perez, et al. Transcriptome innovations in primates revealed by single-molecule long-read sequencing.
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T. L. Cole, C. Zhou, M. Fang, H. Pan, D. T. Ksepka, S. R. Fiddaman, et al. Genomic insights into the secondary aquatic transition of penguins.
Nat Commun
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Li, Y., Liu, Z., Liu, C., et al. HGT is widespread in insects and contributes to male courtship in lepidopterans.
Cell
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Q. Li, M. Wang, P. Zhang, Y. Liu, Q. Guo, Y. Zhu, et al. A single-cell transcriptomic atlas tracking the neural basis of division of labour in an ant superorganism.
Nat Ecol Evol
6, 1191–1204 (2022).
Y. Mao and G. Zhang. A complete, telomere-to-telomere human genome sequence presents new opportunities for evolutionary genomics.
Nat Methods
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Y. Wang, R. B. Gasser, D. Charlesworth and Q. Zhou. Evolution of sexual systems, sex chromosomes and sex-linked gene transcription in flatworms and roundworms.
Nat Commun
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S. Feng, M. Bai, I. Rivas-Gonzalez, C. Li, S. Liu, Y. Tong, et al. Incomplete lineage sorting and phenotypic evolution in marsupials.
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