On the ancestry and evolution of the extinct dire wolf

Gregory L. Gedman; Kathleen Morrill Pirovich; Jonas Oppenheimer; Chaz Hyseni; Molly Cassatt-Johnstone; Nicolas Alexandre; William Troy; Chris Chao; Olivier Fedrigo; Savannah J. Hoyt; Patrick G.S. Grady; Sam Sacco; William Seligmann; Ayusman Dash; Mithil Chokshi; Laura Knecht; James B. Papizan; Tyler Miyawaki; Sven Bocklandt; James Kelher; Sara Ord; Audrey T. Lin; Brandon R. Peecook; Angela Perri; Mikkel-Holger S. Sinding; Greger Larson; Julie Meachen; Love Dalén; Bridgett VonHoldt; M Thomas P Gilbert; Christopher E. Mason; Rachel J. O’Neill; Elinor K. Karlsson; Brandi L. Cantarel; George R. R. Martin; George Church; Ben Lamm; Beth Shapiro

doi:10.1101/2025.04.09.647074

On the ancestry and evolution of the extinct dire wolf

Gregory L. Gedman, Kathleen Morrill Pirovich, Jonas Oppenheimer, Chaz Hyseni, Molly Cassatt-Johnstone, Nicolas Alexandre, William Troy, Chris Chao, Olivier Fedrigo, Savannah J. Hoyt, Patrick G.S. Grady, Sam Sacco, William Seligmann, Ayusman Dash, Mithil Chokshi, Laura Knecht, James B. Papizan, Tyler Miyawaki, Sven Bocklandt, James KelherSara Ord, Audrey T. Lin, Brandon R. Peecook, Angela Perri, Mikkel-Holger S. Sinding, Greger Larson, Julie Meachen, Love Dalén, Bridgett VonHoldt, M Thomas P Gilbert, Christopher E. Mason, Rachel J. O’Neill, Elinor K. Karlsson, Brandi L. Cantarel, George R. R. Martin, George Church, Ben Lamm, Beth Shapiro

Publikation: Working paper › Preprint

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Abstract

Dire wolves (Aenocyon dirus) are extinct predators of Pleistocene North America. Although phenotypically similar to living wolves (Canis lupus), dire wolves have yet to be placed confidently in the canid family tree. We generated 3.4× and 12.8× paleogenomes from two well-preserved dire wolves dating to > 13,000 and > 72,000 years ago, and estimated consensus species trees for these and 10 canid species. Our results revealed that ∼2/3 of dire wolf ancestry is derived from a lineage sister to the clade comprising the gray wolf, coyote, and dhole, and the remaining ∼1/3 from a lineage near the base of Canini diversity. We identified 80 genes evolving under diversifying selection in dire wolves. Our results underscore the power of paleogenomes to resolve long-standing taxonomic questions and contribute to growing evidence of the role of post-speciation gene flow as an evolutionary force.

Originalsprog	Engelsk
Udgiver	bioRxiv
Antal sider	42
DOI	https://doi.org/10.1101/2025.04.09.647074
Status	Udgivet - 2025

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10.1101/2025.04.09.647074Licens: CC BY-NC-ND

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Gedman, G. L., Pirovich, K. M., Oppenheimer, J., Hyseni, C., Cassatt-Johnstone, M., Alexandre, N., Troy, W., Chao, C., Fedrigo, O., Hoyt, S. J., Grady, P. G. S., Sacco, S., Seligmann, W., Dash, A., Chokshi, M., Knecht, L., Papizan, J. B., Miyawaki, T., Bocklandt, S., ... Shapiro, B. (2025). On the ancestry and evolution of the extinct dire wolf. bioRxiv. https://doi.org/10.1101/2025.04.09.647074

Gedman, GL, Pirovich, KM, Oppenheimer, J, Hyseni, C, Cassatt-Johnstone, M, Alexandre, N, Troy, W, Chao, C, Fedrigo, O, Hoyt, SJ, Grady, PGS, Sacco, S, Seligmann, W, Dash, A, Chokshi, M, Knecht, L, Papizan, JB, Miyawaki, T, Bocklandt, S, Kelher, J, Ord, S, Lin, AT, Peecook, BR, Perri, A, Sinding, M-HS, Larson, G, Meachen, J, Dalén, L, VonHoldt, B, Gilbert, MTP, Mason, CE, O’Neill, RJ, Karlsson, EK, Cantarel, BL, Martin, GRR, Church, G, Lamm, B & Shapiro, B 2025 'On the ancestry and evolution of the extinct dire wolf' bioRxiv. https://doi.org/10.1101/2025.04.09.647074

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abstract = "Dire wolves (Aenocyon dirus) are extinct predators of Pleistocene North America. Although phenotypically similar to living wolves (Canis lupus), dire wolves have yet to be placed confidently in the canid family tree. We generated 3.4× and 12.8× paleogenomes from two well-preserved dire wolves dating to > 13,000 and > 72,000 years ago, and estimated consensus species trees for these and 10 canid species. Our results revealed that ∼2/3 of dire wolf ancestry is derived from a lineage sister to the clade comprising the gray wolf, coyote, and dhole, and the remaining ∼1/3 from a lineage near the base of Canini diversity. We identified 80 genes evolving under diversifying selection in dire wolves. Our results underscore the power of paleogenomes to resolve long-standing taxonomic questions and contribute to growing evidence of the role of post-speciation gene flow as an evolutionary force.",

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AU - Pirovich, Kathleen Morrill

AU - Oppenheimer, Jonas

AU - Hyseni, Chaz

AU - Cassatt-Johnstone, Molly

AU - Alexandre, Nicolas

AU - Troy, William

AU - Chao, Chris

AU - Fedrigo, Olivier

AU - Hoyt, Savannah J.

AU - Grady, Patrick G.S.

AU - Sacco, Sam

AU - Seligmann, William

AU - Dash, Ayusman

AU - Chokshi, Mithil

AU - Knecht, Laura

AU - Papizan, James B.

AU - Miyawaki, Tyler

AU - Bocklandt, Sven

AU - Kelher, James

AU - Ord, Sara

AU - Lin, Audrey T.

AU - Peecook, Brandon R.

AU - Perri, Angela

AU - Sinding, Mikkel-Holger S.

AU - Larson, Greger

AU - Meachen, Julie

AU - Dalén, Love

AU - VonHoldt, Bridgett

AU - Gilbert, M Thomas P

AU - Mason, Christopher E.

AU - O’Neill, Rachel J.

AU - Karlsson, Elinor K.

AU - Cantarel, Brandi L.

AU - Martin, George R. R.

AU - Church, George

AU - Lamm, Ben

AU - Shapiro, Beth

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AB - Dire wolves (Aenocyon dirus) are extinct predators of Pleistocene North America. Although phenotypically similar to living wolves (Canis lupus), dire wolves have yet to be placed confidently in the canid family tree. We generated 3.4× and 12.8× paleogenomes from two well-preserved dire wolves dating to > 13,000 and > 72,000 years ago, and estimated consensus species trees for these and 10 canid species. Our results revealed that ∼2/3 of dire wolf ancestry is derived from a lineage sister to the clade comprising the gray wolf, coyote, and dhole, and the remaining ∼1/3 from a lineage near the base of Canini diversity. We identified 80 genes evolving under diversifying selection in dire wolves. Our results underscore the power of paleogenomes to resolve long-standing taxonomic questions and contribute to growing evidence of the role of post-speciation gene flow as an evolutionary force.

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