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Research: Ancient dog introgression into the Iberian wolf genome may have facilitated adaptation to human-dominated landscapes
- Diana Lobo,
- Hernán E. Morales,
- Cock Van Oosterhout,
- José Vicente López-Bao,
- Pedro Silva,
- Luis Llaneza,
- Carolina Pacheco,
- Diana Castro,
- Germán Hernández-Alonso,
- George Pacheco,
- John Archer,
- M. Thomas P. Gilbert,
- Nuno Ferrand,
- and Raquel Godinho
Genome Res. March 2025 35: 432-445; Published in Advance February 14, 2025, doi:10.1101/gr.279093.124
..., some species managed to change their behavior and ecology to adapt to human activities in human-dominated landscapes (Benazzo et al. 2017). A remarkable example of such resilience is illustrated by some populations of the Eurasian gray wolf (Canis lupus) living in highly human-dominated landscapes...
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Research: Birth of protein-coding exons by ancient domestication of LINE-1 retrotransposon
- Koichi Kitao,
- Kenji Ichiyanagi,
- and So Nakagawa
Genome Res. June 2025 35: 1287-1300; Published in Advance May 8, 2025, doi:10.1101/gr.280007.124
...in populations and determine their degree of evolutionary conservation over time.In this study, we identified the exonized L1 elements that give rise to ORF1p fusion proteins and are evolutionarily conserved in vertebrate s for periods ranging from tens of millions to more than 280 million years. These findings...
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Method: Seamless, rapid, and accurate analyses of outbreak genomic data using split k-mer analysis
- Romain Derelle,
- Johanna von Wachsmann,
- Tommi Mäklin,
- Joel Hellewell,
- Timothy Russell,
- Ajit Lalvani,
- Leonid Chindelevitch,
- Nicholas J. Croucher,
- Simon R. Harris,
- and John A. Lees
Genome Res. October 2024 34: 1661-1673; Published in Advance October 15, 2024, doi:10.1101/gr.279449.124
...to a faster dictionary implementation, optimized file parsing, and use of a faster serialization process. Parallelization is not directly supported in SKA1.Split k-mers accurately and quickly genotype closely related samplesBefore using SKA2 to analyze bacterial populations, we first used two...
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Research: Multi-species analysis of inflammatory response elements reveals ancient and lineage-specific contributions of transposable elements to NF-kB binding
- Liangxi Wang,
- Tiegh Taylor,
- Kumaragurubaran Rathnakumar,
- Nadiya Khyzha,
- Minggao Liang,
- Azad Alizada,
- Laura F. Campitelli,
- Sara E. Pour,
- Zain M. Patel,
- Lina Antounians,
- Ian C. Tobias,
- Huayun Hou,
- Timothy R. Hughes,
- Sushmita Roy,
- Jennifer A. Mitchell,
- Jason E. Fish,
- and Michael D. Wilson
Genome Res. July 2025 35: 1544-1559; Published in Advance June 6, 2025, doi:10.1101/gr.280357.124
...decayed during early primate evolution (>50 million years ago [MYA]) before stabilizing since the separation of Old World monkeys (<50 MYA). Taken together, our results suggest ancient and lineage-specific transposon subfamilies contributed to mammalian NF-kB regulatory networks.Transposable elements (TEs...
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Resource: Full-length RNA transcript sequencing traces brain isoform diversity in house mouse natural populations
- Wenyu Zhang,
- Anja Guenther,
- Yuanxiao Gao,
- Kristian Ullrich,
- Bruno Huettel,
- Aftab Ahmad,
- Lei Duan,
- Kaizong Wei,
- and Diethard Tautz
Genome Res. November 2024 34: 2118-2132; Published in Advance September 17, 2024, doi:10.1101/gr.279166.124
...nucleotide polymorphism (SNP) diversity between the populations. We find that ancient housekeeping genes are a major source of the overall isoform diversity, and that the generation of alternative first exons plays a major role in generating new isoforms. Given that our data allow us to distinguish between...
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Method: Three assays for in-solution enrichment of ancient human DNA at more than a million SNPs
- Nadin Rohland,
- Swapan Mallick,
- Matthew Mah,
- Robert Maier,
- Nick Patterson,
- and David Reich
Genome Res. November/December 2022 32: 2068-2078; Published in Advance December 14, 2022, doi:10.1101/gr.276728.122
...://arborbiosci.com/wp-content/uploads/2021/03/Skoglund_Ancestral_850K_Panel_ Design.pdf). These sites were chosen to reduce bias in population genetic analysis as the primarily Eurasian ancestry of the individuals in whom SNPs are discovered can skew statistics when studying African population history (Bergström et al. 2020). Transversion...
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Research: Experimentally evolving Drosophila erecta populations may fail to establish an effective piRNA-based host defense against invading P-elements
- Divya Selvaraju,
- Filip Wierzbicki,
- and Robert Kofler
Genome Res. March 2024 34: 410-425; Published in Advance March 15, 2024, doi:10.1101/gr.278706.123
...Divya Selvaraju1,2, Filip Wierzbicki1,2 and Robert Kofler1 1Institut für Populationsgenetik, Vetmeduni Vienna, 1210 Vienna, Austria; 2Vienna Graduate School of Population Genetics, Vetmeduni Vienna, 1210 Vienna, Austria Corresponding author: rokofler@gmail.comAbstractTo prevent the spread...
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Research: Reconstructing genetic history of Siberian and Northeastern European populations
- Emily H.M. Wong,
- Andrey Khrunin,
- Larissa Nichols,
- Dmitry Pushkarev,
- Denis Khokhrin,
- Dmitry Verbenko,
- Oleg Evgrafov,
- James Knowles,
- John Novembre,
- Svetlana Limborska,
- and Anton Valouev
Genome Res. January 2017 27: 1-14; Published in Advance December 13, 2016, doi:10.1101/gr.202945.115
...with additional 32 modern-day and 46 ancient human s to reconstruct genetic histories of several indigenous Northern Eurasian populations. We found that Siberian and East Asian populations shared 38% of their ancestry with a 45,000-yr-old Ust’-Ishim individual who was previously believed to have no modern...
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Method: A minimally destructive protocol for DNA extraction from ancient teeth
- Éadaoin Harney,
- Olivia Cheronet,
- Daniel M. Fernandes,
- Kendra Sirak,
- Matthew Mah,
- Rebecca Bernardos,
- Nicole Adamski,
- Nasreen Broomandkhoshbacht,
- Kimberly Callan,
- Ann Marie Lawson,
- Jonas Oppenheimer,
- Kristin Stewardson,
- Fatma Zalzala,
- Alexandra Anders,
- Francesca Candilio,
- Mihai Constantinescu,
- Alfredo Coppa,
- Ion Ciobanu,
- János Dani,
- Zsolt Gallina,
- Francesco Genchi,
- Emese Gyöngyvér Nagy,
- Tamás Hajdu,
- Magdolna Hellebrandt,
- Antónia Horváth,
- Ágnes Király,
- Krisztián Kiss,
- Barbara Kolozsi,
- Péter Kovács,
- Kitti Köhler,
- Michaela Lucci,
- Ildikó Pap,
- Sergiu Popovici,
- Pál Raczky,
- Angela Simalcsik,
- Tamás Szeniczey,
- Sergey Vasilyev,
- Cristian Virag,
- Nadin Rohland,
- David Reich,
- and Ron Pinhasi
Genome Res. March 2021 31: 472-483; Published in Advance February 12, 2021, doi:10.1101/gr.267534.120
...methods using a variety of metrics. First, we compare the rate of matching to the mitochondrial consensus sequence (Fu et al. 2013). A minimum threshold of 95% is typically applied during screening of ancient DNA for population genetic studies. We observe substantial variability in contamination rate...
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Method: Human auditory ossicles as an alternative optimal source of ancient DNA
- Kendra Sirak,
- Daniel Fernandes,
- Olivia Cheronet,
- Eadaoin Harney,
- Matthew Mah,
- Swapan Mallick,
- Nadin Rohland,
- Nicole Adamski,
- Nasreen Broomandkhoshbacht,
- Kimberly Callan,
- Francesca Candilio,
- Ann Marie Lawson,
- Kirsten Mandl,
- Jonas Oppenheimer,
- Kristin Stewardson,
- Fatma Zalzala,
- Alexandra Anders,
- Juraj Bartík,
- Alfredo Coppa,
- Tumen Dashtseveg,
- Sándor Évinger,
- Zdeněk Farkaš,
- Tamás Hajdu,
- Jamsranjav Bayarsaikhan,
- Lauren McIntyre,
- Vyacheslav Moiseyev,
- Mercedes Okumura,
- Ildikó Pap,
- Michael Pietrusewsky,
- Pál Raczky,
- Alena Šefčáková,
- Andrei Soficaru,
- Tamás Szeniczey,
- Béla Miklós Szőke,
- Dennis Van Gerven,
- Sergey Vasilyev,
- Lynne Bell,
- David Reich,
- and Ron Pinhasi
Genome Res. March 2020 30: 427-436; Published in Advance February 25, 2020, doi:10.1101/gr.260141.119
...of selection in 230 ancient Eurasians. Nature 528: 499–503. doi:10.1038/nature16152 ↵Mays S, Elders J, Humphrey L, White W, Marshall P. 2013. Science and the dead: a guideline for the destructive sampling of archaeological human remains for scientific analysis. Advisory Panel on the Archaeology of Burials...

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