Searching journal content for articles similar to Zhang et al. 14 (5): 845.

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  1. Research: Independent expansion, selection, and hypervariability of the TBC1D3 gene family in humans
    • Xavi Guitart,
    • David Porubsky,
    • DongAhn Yoo,
    • Max L. Dougherty,
    • Philip C. Dishuck,
    • Katherine M. Munson,
    • Alexandra P. Lewis,
    • Kendra Hoekzema,
    • Jordan Knuth,
    • Stephen Chang,
    • Tomi Pastinen,
    • and Evan E. Eichler
    Genome Res. November 2024 34: 1798-1810; Published in Advance August 6, 2024, doi:10.1101/gr.279299.124
    ...conversion of all gene family copies in each lineage. In contrast, the gelada and rhesus macaque show both shared and lineage-specific groups, suggesting TBC1D3 expanded before and after speciation. Using 25 and 6.5 million years ago (mya) as times of human–macaque and human–chimpanzee divergence, we...
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  2. Research: Speciation network in Laurasiatheria: retrophylogenomic signals
    • Liliya Doronina,
    • Gennady Churakov,
    • Andrej Kuritzin,
    • Jingjing Shi,
    • Robert Baertsch,
    • Hiram Clawson,
    • and Jürgen Schmitz
    Genome Res. June 2017 27: 997-1003; Published in Advance March 15, 2017, doi:10.1101/gr.210948.116
    ..., different histories can be embedded in the , and depending on the region analyzed, can provide one or the other topology in tree reconstruction (e.g., 23% of the human does not show that chimpanzee is our closest relative) (Ebersberger et al. 2007). Thus, in clades with rapidly diversifying species...
  3. Research: Gene regulation and speciation in house mice
    • Katya L. Mack,
    • Polly Campbell,
    • and Michael W. Nachman
    Genome Res. April 2016 26: 451-461; Published in Advance February 1, 2016, doi:10.1101/gr.195743.115
    ...between chimpanzees and humans could not be explained by changes in protein sequences alone (King andWilson 1975). Since then, there has been a lively debate about the relative importance of changes in gene regulation versus changes in gene structure in adaptive evolution (e.g., Hoekstra and Coyne 2007...
  4. Method: Identifying chromosomal subpopulations based on their recombination histories advances the study of the genetic basis of phenotypic traits
    • Carlos Ruiz-Arenas,
    • Alejandro Cáceres,
    • Marcos López,
    • Dolors Pelegrí-Sisó,
    • Josefa González,
    • and Juan R. González
    Genome Res. December 2020 30: 1802-1814; Published in Advance November 17, 2020, doi:10.1101/gr.258301.119
    ...in Drosophila melanogaster and human, and the chromosomes under selective pressure at the lactase locus in humans. We then applied recombClust to the complex human 1q21.1 region, where nonallelic homologous recombination produces deleterious phenotypes. We discovered and validated the presence of two different...
  5. Research: Positive selection in noncoding genomic regions of vocal learning birds is associated with genes implicated in vocal learning and speech functions in humans
    • James A. Cahill,
    • Joel Armstrong,
    • Alden Deran,
    • Carolyn J. Khoury,
    • Benedict Paten,
    • David Haussler,
    • and Erich D. Jarvis
    Genome Res. November 2021 31: 2035-2049; Published in Advance October 19, 2021, doi:10.1101/gr.275989.121
    .... To explore this hypothesis at the level of targets of selection, we tested for AR convergence between vocal learning birds and humans. We compiled human ARs from five studies (Lindblad-Toh et al. 2005; Pollard et al. 2006; Prabhakar et al. 2006; Bird et al. 2007; Gittelman et al. 2015), for a total of 3134...
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  6. Method: Greater strength of selection and higher proportion of beneficial amino acid changing mutations in humans compared with mice and Drosophila melanogaster
    • Ying Zhen,
    • Christian D. Huber,
    • Robert W. Davies,
    • and Kirk E. Lohmueller
    Genome Res. January 2021 31: 110-120; Published in Advance November 18, 2020, doi:10.1101/gr.256636.119
    ...for weakly beneficial mutations segregating as polymorphisms infer slightly higher values of α = 0.24 between humans and chimpanzee and α = 0.135 in the human lineage (Galtier 2016; Uricchio et al. 2019). In addition, population sizes of the outgroup and ancestral population determine the rate of fixation...
  7. Research: Error-prone polymerase activity causes multinucleotide mutations in humans
    • Kelley Harris and
    • Rasmus Nielsen
    Genome Res. September 2014 24: 1445-1454; Published in Advance July 30, 2014, doi:10.1101/gr.170696.113
    ...Error-prone polymerase activity causes multinucleotide mutations in humans Kelley Harris 1 and Rasmus Nielsen 2 , 3 , 4 1 Department of Mathematics, University of California Berkeley, Berkeley, California 94703, USA; 2 Department...
  8. Perspective: Evolution under canalization and the dual roles of microRNAs—A hypothesis
    • Chung-I Wu,
    • Yang Shen,
    • and Tian Tang
    Genome Res. May 2009 19: 734-743; doi:10.1101/gr.084640.108
    ...’s (which should be reflected in their -wide Ka/Ks ratio). Nevertheless, the emergence rate of miRNAs in Drosophila does not appear to be lower than that in human or chimpanzee (Berezikov et al. 2006; Lu et al. 2008b). Given the much larger Ne, as well as the smaller , the high rate of miRNA emergence...
  9. Methods: A new approach to estimate parameters of speciation models with application to apes
    • Celine Becquet and
    • Molly Przeworski
    Genome Res. October 2007 17: 1505-1519; Published in Advance August 21, 2007, doi:10.1101/gr.6409707
    ...–920 Kya, suggesting that speciation occurred after the formation of the River Congo, 1.5–3.5 Mya. These estimates do not take into account possible error in the mutation rate per year. But even if we consider a time to the most recent common ancestor between human and chimpanzee at the upper limit of what...
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  10. Methods: Recovering the geographic origin of early modern humans by realistic and spatially explicit simulations
    • Nicolas Ray,
    • Mathias Currat,
    • Pierre Berthier,
    • and Laurent Excoffier
    Genome Res. August 2005 15: 1161-1167; doi:10.1101/gr.3708505
    ...-Sforza and Feldman 2003 ; Currat and Excoffier 2004 ). This is mainly based on the observation of earliest forms of anatomically modern humans in Africa ( White et al. 2003 ) and a very recent common ancestry of mitochondrial ( Vigilant et al. 1991 ; Ingman et al. 2000 ) and Y-chromosome ( Donnelly et al. 1996...
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