Searching journal content for articles similar to Oliver et al. 17 (5): 594.

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  1. Research: Stable genome structures in living fossil fishes
    • Cheng Wang,
    • Chase D. Brownstein,
    • Wenjun Chen,
    • Zufa Ding,
    • Dan Yu,
    • Yu Deng,
    • Chenguang Feng,
    • Thomas J. Near,
    • Shunping He,
    • and Liandong Yang
    Genome Res. February 2026 36: 318-329; Published in Advance January 13, 2026, doi:10.1101/gr.280800.125
    ...contributed equally to this work. Corresponding authors: thomas.near@yale.edu, clad@ihb.ac.cn, yangliandong1987@163.comAbstractGenomic evolution can propel and restrict species diversification. Rapid molecular evolution and genomic rearrangement is often associated with increased species diversification...
  2. Research: The grasshopper genome reveals long-term gene content conservation of the X Chromosome and temporal variation in X Chromosome evolution
    • Xinghua Li,
    • Judith E. Mank,
    • and Liping Ban
    Genome Res. July 2024 34: 997-1007; Published in Advance August 5, 2024, doi:10.1101/gr.278794.123
    ...conservation of the X Chromosome gene content across broad swathes of the insect phylogeny, as well as temporal dynamics to the rate of X Chromosome evolution (Meisel et al. 2019; Chauhan et al. 2021).ResultsGenome featuresWe used PacBio HiFi sequencing to generate sequences for a female (XX) migratory locust...
  3. Resource: High-quality assembly of the Chinese white truffle genome and recalibrated divergence time estimate provide insight into the evolutionary dynamics of Tuberaceae
    • Jacopo Martelossi,
    • Jacopo Vujovic,
    • Yue Huang,
    • Alessia Tatti,
    • Kaiwei Xu,
    • Federico Puliga,
    • Yuanxue Chen,
    • Omar Rota Stabelli,
    • Fabrizio Ghiselli,
    • Xiaoping Zhang,
    • and Alessandra Zambonelli
    Genome Res. November 2025 35: 2601-2616; Published in Advance August 21, 2025, doi:10.1101/gr.280368.124
    ...constitute a principal driver of evolution, shaping its architecture and regulatory networks. In this context, Tuberaceae can become an important model system to study their genomic impact; however, the family lacks high-quality assemblies. Here, we investigate the interplay between TEs and Tuberaceae...
  4. Research: Tempo and mode of regulatory evolution in Drosophila
    • Joseph D. Coolon,
    • C. Joel McManus,
    • Kraig R. Stevenson,
    • Brenton R. Graveley,
    • and Patricia J. Wittkopp
    Genome Res. May 2014 24: 797-808; Published in Advance February 24, 2014, doi:10.1101/gr.163014.113
    ...from positive selection in this lineage. Taken together, this work reveals not only the rate at which gene expression evolves, but also the molecular and evolutionary mechanisms responsible for this evolution.Understanding the relationship between tempo (the rate at which a trait evolves) and mode (the...
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  5. Research: Rapid evolution of piRNA clusters in the Drosophila melanogaster ovary
    • Satyam P. Srivastav,
    • Cédric Feschotte,
    • and Andrew G. Clark
    Genome Res. May 2024 34: 711-724; Published in Advance May 15, 2024, doi:10.1101/gr.278062.123
    ...in Drosophila melanogaster, much less is known about the origin and evolution of piCs in this or any other species. To investigate piC origin and evolution, we use a population genomic approach to compare piC activity and sequence composition across eight geographically distant strains of D. melanogaster...
  6. Research: Evolution of genome structure in the Drosophila simulans species complex
    • Mahul Chakraborty,
    • Ching-Ho Chang,
    • Danielle E. Khost,
    • Jeffrey Vedanayagam,
    • Jeffrey R. Adrion,
    • Yi Liao,
    • Kristi L. Montooth,
    • Colin D. Meiklejohn,
    • Amanda M. Larracuente,
    • and J.J. Emerson
    Genome Res. March 2021 31: 380-396; Published in Advance February 9, 2021, doi:10.1101/gr.263442.120
    ..., underlies phenotypic evolution and contributes to hybrid incompatibilities between species. However, repetitive genomic regions are fragmented and misassembled in most contemporary assemblies. We generated highly contiguous de novo reference s for the Drosophila simulans species complex (D. simulans, D...
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  7. Resource: A new emu genome illuminates the evolution of genome configuration and nuclear architecture of avian chromosomes
    • Jing Liu,
    • Zongji Wang,
    • Jing Li,
    • Luohao Xu,
    • Jiaqi Liu,
    • Shaohong Feng,
    • Chunxue Guo,
    • Shengchan Chen,
    • Zhanjun Ren,
    • Jinpeng Rao,
    • Kai Wei,
    • Yuezhou Chen,
    • Erich D. Jarvis,
    • Guojie Zhang,
    • and Qi Zhou
    Genome Res. March 2021 31: 497-511; Published in Advance January 6, 2021, doi:10.1101/gr.271569.120
    ...window Figure 2. Tempo of avian chromosome evolution. (A–D) Genomic synteny between green sea turtle, rattlesnake, American alligator versus emu and green sea turtle versus golden eagle, respectively. Chromosome names with blue/red color denote the fused chromosomes in reptiles and the homologous...
  8. Research: The Chinese longsnout catfish genome provides novel insights into the feeding preference and corresponding metabolic strategy of carnivores
    • Yulong Liu,
    • Gang Zhai,
    • Jingzhi Su,
    • Yulong Gong,
    • Bingyuan Yang,
    • Qisheng Lu,
    • Longwei Xi,
    • Yutong Zheng,
    • Jingyue Cao,
    • Haokun Liu,
    • Junyan Jin,
    • Zhimin Zhang,
    • Yunxia Yang,
    • Xiaoming Zhu,
    • Zhongwei Wang,
    • Gaorui Gong,
    • Jie Mei,
    • Zhan Yin,
    • Rodolphe E. Gozlan,
    • Shouqi Xie,
    • and Dong Han
    Genome Res. July 2024 34: 981-996; Published in Advance August 9, 2024, doi:10.1101/gr.278476.123
    ...; Dai et al. 2022). Therefore, we sequenced and assembled the whole of L. longirostris. We obtained candidate genes using whole- sequencing of Chinese longsnout catfish, as well as comparative genomics of carnivorous and herbivorous fish through a joint analysis of positive selection and rapid evolution...
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  9. Methods: Estimating the tempo and mode of gene family evolution from comparative genomic data
    • Matthew W. Hahn,
    • Tijl De Bie,
    • Jason E. Stajich,
    • Chi Nguyen,
    • and Nello Cristianini
    Genome Res. August 2005 15: 1153-1160; doi:10.1101/gr.3567505
    ...Estimating the tempo and mode of gene family evolution from comparative genomic data Matthew W. Hahn 1 , 6 , 7 , Tijl De Bie 4 , 6 , Jason E. Stajich 5 , Chi Nguyen 2 , and Nello Cristianini 3 1 Center for Population...
  10. Research: Integrated analysis sheds light on evolutionary trajectories of young transcription start sites in the human genome
    • Cai Li,
    • Boris Lenhard,
    • and Nicholas M. Luscombe
    Genome Res. May 2018 28: 676-688; Published in Advance April 4, 2018, doi:10.1101/gr.231449.117
    ...into the tempo and mode of regulatory evolution of TSSs.In our analysis, we examined only cis-regulatory variants around TSS loci, as published trans-regulatory variants are rare and of relatively low quality. Since the density of cis-regulatory variants drops rapidly with increasing distances (The GTEx...
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