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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
...Africa Corresponding authors: diana.lobo@cibio.up.pt, rgodinho@cibio.up.ptAbstractUnderstanding how large carnivores respond to increasingly human-dominated landscapes will determine their future adaptive potential. The Iberian wolf (Canis lupus signatus), a gray wolf subspecies endemic to the Iberian...
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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
...from Africa. Proc Natl Acad Sci 115: 4128–4133. doi:10.1073/pnas.1717873115 ↵Prendergast ME, Sawchuk E. 2018. Boots on the ground in Africa's ancient DNA ‘revolution’: archaeological perspectives on ethics and best practices. Antiquity 92: 803–815. doi:10.15184/aqy.2018.70 ↵Prendergast ME, Lipson M...
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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
...’-Ishim settlement in Western Siberia (Fu et al. 2014). The Ust’-Ishim’s provided evidence for ancient human and Neanderthal admixture that occurred ∼50–60 kya (Fu et al. 2014). Other ancient human sites in Siberia yielded ancient DNA from ancient North Eurasians (ANEs) (Lazaridis et al. 2014), including the Upper...
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Research: Indigenous Arabs are descendants of the earliest split from ancient Eurasian populations
- Juan L. Rodriguez-Flores,
- Khalid Fakhro,
- Francisco Agosto-Perez,
- Monica D. Ramstetter,
- Leonardo Arbiza,
- Thomas L. Vincent,
- Amal Robay,
- Joel A. Malek,
- Karsten Suhre,
- Lotfi Chouchane,
- Ramin Badii,
- Ajayeb Al-Nabet Al-Marri,
- Charbel Abi Khalil,
- Mahmoud Zirie,
- Amin Jayyousi,
- Jacqueline Salit,
- Alon Keinan,
- Andrew G. Clark,
- Ronald G. Crystal,
- and Jason G. Mezey
Genome Res. February 2016 26: 151-162; Published in Advance January 4, 2016, doi:10.1101/gr.191478.115
...coverage, including 56 of indigenous Arab ancestry. The indigenous Arab s defined a cluster distinct from other ancestral groups, and these s showed clear hallmarks of an ancient out-of-Africa bottleneck. Similar to other Middle Eastern populations, the indigenous Arabs had higher levels of Neanderthal...
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Resource: An unbiased resource of novel SNP markers provides a new chronology for the human Y chromosome and reveals a deep phylogenetic structure in Africa
- Rosaria Scozzari,
- Andrea Massaia,
- Beniamino Trombetta,
- Giovanna Bellusci,
- Natalie M. Myres,
- Andrea Novelletto,
- and Fulvio Cruciani
Genome Res. March 2014 24: 535-544; Published in Advance January 6, 2014, doi:10.1101/gr.160788.113
...and often from small remote populations has also made their study difficult. Yet, deep-rooted lineages are particularly informative in the reconstruction of the scenario of an ancient population structuring in Africa. This is currently considered to be the source of global patterns of -wide diversity under...
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Method: True single-molecule DNA sequencing of a pleistocene horse bone
- Ludovic Orlando,
- Aurelien Ginolhac,
- Maanasa Raghavan,
- Julia Vilstrup,
- Morten Rasmussen,
- Kim Magnussen,
- Kathleen E. Steinmann,
- Philipp Kapranov,
- John F. Thompson,
- Grant Zazula,
- Duane Froese,
- Ida Moltke,
- Beth Shapiro,
- Michael Hofreiter,
- Khaled A.S. Al-Rasheid,
- M. Thomas P. Gilbert,
- and Eske Willerslev
Genome Res. October 2011 21: 1705-1719; Published in Advance July 29, 2011, doi:10.1101/gr.122747.111
...-eighties, when short mitochondrial DNA (mtDNA) fragments were successfully cloned and sequenced from museum specimens of the quagga (Equus quagga)—an equid that became extinct in South Africa at the end of the 19th century. The findings demonstrated that trace nucleic acids survive at least over the time frame...
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LETTER: Mitochondrial Genome Variation in Eastern Asia and the Peopling of Japan
- Masashi Tanaka,
- Vicente M. Cabrera,
- Ana M. González,
- José M. Larruga,
- Takeshi Takeyasu,
- Noriyuki Fuku,
- Li-Jun Guo,
- Raita Hirose,
- Yasunori Fujita,
- Miyuki Kurata,
- Ken-ichi Shinoda,
- Kazuo Umetsu,
- Yoshiji Yamada,
- Yoshiharu Oshida,
- Yuzo Sato,
- Nobutaka Hattori,
- Yoshikuni Mizuno,
- Yasumichi Arai,
- Nobuyoshi Hirose,
- Shigeo Ohta,
- Osamu Ogawa,
- Yasushi Tanaka,
- Ryuzo Kawamori,
- Masayo Shamoto-Nagai,
- Wakako Maruyama,
- Hiroshi Shimokata,
- Ryota Suzuki,
- and Hidetoshi Shimodaira
Genome Res. October 2004 14: 1832-1850; doi:10.1101/gr.2286304
...this complex picture. Recent analysis of global mitochondrial DNA diversity in humans based on complete mtDNA sequences has provided compelling evidence of a human mtDNA origin in Africa ( Ingman et al. 2000 ). Less than 100,000 years ago, at least two mtDNA human lineages began to rapidly spread from Africa...
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LETTER: AluInsertion Polymorphisms and Human Evolution: Evidence for a Larger Population Size in Africa
- Mark Stoneking,
- Jennifer J. Fontius,
- Stephanie L. Clifford,
- Himla Soodyall,
- Santosh S. Arcot,
- Nilmani Saha,
- Trefor Jenkins,
- Mohammad A. Tahir,
- Prescott L. Deininger,
- and Mark A. Batzer
Genome Res. November 1, 1997 7: 1061-1071; doi:10.1101/gr.7.11.1061
...between populations and 87% is found within populations. For comparing patterns of variation among populations, we grouped the 34 populations into 6 geographic regions, consisting of Africa, Europe, Western Asia, Southeast Asia, Sahul (Australia and New Guinea), and the Americas (Table 1 b). The average...
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Review: Recent advances in methods to characterize archaic introgression in modern humans
- David Peede,
- Mayra M. Bañuelos,
- Jazeps Medina Tretmanis,
- Miriam Miyagi,
- and Emilia Huerta-Sánchez
Genome Res. February 2026 36: 239-256; Published in Advance January 16, 2026, doi:10.1101/gr.278993.124
...introgression presents unique challenges, particularly because of the limitations of ancient DNA (aDNA) sequencing. Although extensive genomic data exists for modern populations (The 1000 Genomes Project Consortium 2015; Mallick et al. 2016; Bergström et al. 2020; Byrska-Bishop et al. 2022), high...
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Research: The peopling of South America and the trans-Andean gene flow of the first settlers
- Alberto Gómez-Carballa,
- Jacobo Pardo-Seco,
- Stefania Brandini,
- Alessandro Achilli,
- Ugo A. Perego,
- Michael D. Coble,
- Toni M. Diegoli,
- Vanesa Álvarez-Iglesias,
- Federico Martinón-Torres,
- Anna Olivieri,
- Antonio Torroni,
- and Antonio Salas
Genome Res. June 2018 28: 767-779; Published in Advance May 7, 2018, doi:10.1101/gr.234674.118
...at positions 16182, 16183, and 16519, as well as variation around position 310 and length or point heteroplasmies were not considered for the phylogenetic reconstruction. Mitochondrial DNA sequence data for comparisons, phylogenetic trees, and maps of interpolated frequencies were obtained from the literature...

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