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Research: Small polymorphisms are a source of ancestral bias in structural variant breakpoint placement
- Peter A. Audano and
- Christine R. Beck
Genome Res. January 2024 34: 7-19; Published in Advance January 4, 2024, doi:10.1101/gr.278203.123
...; and deleted bases are gray. The inserted sequence was not found in GRCh38 but was present in nonhuman primates and likely represents the deletion of ancestral sequence where the reference contains the derived (deleted) allele.Many differences in the PGGB SVs are attributable to different breakpoint choices...
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Method: In silico phylogenomics using complete genomes: a case study on the evolution of hominoids
- Igor Rodrigues Costa,
- Francisco Prosdocimi,
- and W. Bryan Jennings
Genome Res. September 2016 26: 1257-1267; Published in Advance July 19, 2016, doi:10.1101/gr.203950.115
...et al. 2007; Thomson et al. 2010), AE loci (Lemmon et al. 2012), or UCE loci (Faircloth et al. 2012). In phylogenomic studies involving populations or species that diverged recently or rapidly, coalescent theory predicts that neutral genomic loci will often have retained ancestral polymorphisms...
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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
...maximum-likelihood analysis with the phytools package (Revell 2012), applying the fastAnc function to reconstruct ancestral states according to divergence times and size. Additionally, we counted the active TE copies for each species and generated a heat map for comparison.Population structure...
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Research: Comparative RNA sequencing reveals substantial genetic variation in endangered primates
- George H. Perry,
- Páll Melsted,
- John C. Marioni,
- Ying Wang,
- Russell Bainer,
- Joseph K. Pickrell,
- Katelyn Michelini,
- Sarah Zehr,
- Anne D. Yoder,
- Matthew Stephens,
- Jonathan K. Pritchard,
- and Yoav Gilad
Genome Res. April 2012 22: 602-610; Published in Advance December 29, 2011, doi:10.1101/gr.130468.111
...populations, because the individuals from these species in our study are from managed laboratory research colonies. Comparative RNA sequencing in endangered primates Genome Research 605 www..org protein might be explained by adaptive nucleotide substitutions that occurred in ancestral primate lineages...
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Research: Transposable elements contribute to the evolution of host shift–related genes in cactophilic Drosophila species
- Daniel Siqueira de Oliveira,
- Anaïs Larue,
- William Vilas Boas Nunes,
- Francois Sabot,
- Alejandra Bodelón,
- María Pilar García Guerreiro,
- Cristina Vieira,
- and Claudia Marcia Aparecida Carareto
Genome Res. March 2026 36: 487-505; Published in Advance February 10, 2026, doi:10.1101/gr.280463.125
...different preferences. Transposable elements are a source of genetic novelty between populations and species, driving rapid adaptive evolution. However, the extent of TEs’ contribution to host shift remains unexplored. Here, we perform genomic and transcriptomic analyses in six s of cactophilic species...
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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
..., and Diptera, and the 800 Mb grasshopper X Chromosome is homologous to the fly ancestral X Chromosome despite 400 million years of divergence, suggesting either repeated origin of sex chromosomes with highly similar gene content, or long-term conservation of the X Chromosome. We use this broad conservation...
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Method: The multicomparative 2-n-way genome suite
- Gennady Churakov,
- Fengjun Zhang,
- Norbert Grundmann,
- Wojciech Makalowski,
- Angela Noll,
- Liliya Doronina,
- and Jürgen Schmitz
Genome Res. October 2020 30: 1508-1516; Published in Advance July 29, 2020, doi:10.1101/gr.262261.120
...2-way alignments. We designed the tool for easy use as an extremely powerful, web-interactive platform. Herein we show the power of 2-n-way with some prime examples spanning the scope of architecture, functional genomics, population genomics, and phylogenomics.ResultsFrom a well-characterized target...
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Method: Variational inference using approximate likelihood under the coalescent with recombination
- Xinhao Liu,
- Huw A. Ogilvie,
- and Luay Nakhleh
Genome Res. November 2021 31: 2107-2119; Published in Advance August 23, 2021, doi:10.1101/gr.273631.120
...2007) and propelled population and phylogenomic inferences to successful applications that span several fields of biology and biomedicine (Siepel 2009; Rogers and Gibbs 2014). Coalescent-based models allow for estimating the values of parameters, including population divergence times, mutation...
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Research: Multiple Pristionchus pacificus genomes reveal distinct evolutionary dynamics between de novo candidates and duplicated genes
- Neel Prabh and
- Christian Rödelsperger
Genome Res. July 2022 32: 1315-1327; Published in Advance May 26, 2022, doi:10.1101/gr.276431.121
...species without being reproductively isolated (McGaughran et al. 2016). The resulting combination of species and population-level phylogenomic data allows us to perform evolutionary comparisons at various timescales and to provide empirical support for the rapid turnover hypothesis...
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Research: Genomic architecture constrained placental mammal X Chromosome evolution
- Wesley A. Brashear,
- Kevin R. Bredemeyer,
- and William J. Murphy
Genome Res. August 2021 31: 1353-1365; Published in Advance July 22, 2021, doi:10.1101/gr.275274.121
.... These authors further suggested that these three primate gene families share a common X-linked ancestor with the murine ampliconic Spanx and Cypt orthologous gene families.In contrast, the mouse X Chromosome possesses only 50% of the ancestral ampliconic CTA gene families (Table 3), having lost orthologs...

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