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For: Schubert M, Ermini L, Der Sarkissian C, Jónsson H, Ginolhac A, Schaefer R, Martin MD, Fernández R, Kircher M, McCue M, Willerslev E, Orlando L. Characterization of ancient and modern genomes by SNP detection and phylogenomic and metagenomic analysis using PALEOMIX. Nat Protoc 2014;9:1056-82. [PMID: 24722405 DOI: 10.1038/nprot.2014.063] [Citation(s) in RCA: 287] [Impact Index Per Article: 26.1] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/21/2022]
Number Cited by Other Article(s)
1
Andrews AJ, Eriksen EF, Star B, Præbel K, Di Natale A, Malca E, Onar V, Aniceti V, Carenti G, Piquès G, Nielsen SV, Persson P, Piattoni F, Fontani F, Atmore LM, Kersten O, Tinti F, Cilli E, Cariani A. Ancient DNA suggests a historical demographic decline and genetic erosion in the Atlantic bluefin tuna. Proc Natl Acad Sci U S A 2025;122:e2409302122. [PMID: 40392844 DOI: 10.1073/pnas.2409302122] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/13/2024] [Accepted: 04/08/2025] [Indexed: 05/22/2025]  Open
2
Miga M, Awg Abdul Rahman A, Parimannan S, Rajandas H, Sitam FT, Tokiman L, Kemalok J, Shamsir MS, Mohd Salleh F. Complete mitochondrial genome data and phylogenetic analysis of the Plain Banded Awl, Hasora vitta (Lepidoptera: Hesperiidae: Coeliadinae) from Malaysia. Mitochondrial DNA B Resour 2025;10:528-531. [PMID: 40433468 PMCID: PMC12107662 DOI: 10.1080/23802359.2025.2509807] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/12/2024] [Accepted: 05/19/2025] [Indexed: 05/29/2025]  Open
3
Grasso G, Debruyne R, Adamo M, Rué O, Lejzerowicz F, Bittner L, Bianciotto V, Marmeisse R. Ancient Microbiomes as Mirrored by DNA Extracted From Century-Old Herbarium Plants and Associated Soil. Mol Ecol Resour 2025:e14122. [PMID: 40411280 DOI: 10.1111/1755-0998.14122] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/21/2024] [Revised: 02/27/2025] [Accepted: 04/30/2025] [Indexed: 05/26/2025]
4
Bro‐Jørgensen MH, Ahlgren H, Glykou A, Ruiz‐Puerta EJ, Lõugas L, Gotfredsen AB, Olsen MT, Lidén K. The Evolutionary History of the Extinct Baltic Sea Harp Seal Population. Ecol Evol 2025;15:e71322. [PMID: 40352621 PMCID: PMC12061552 DOI: 10.1002/ece3.71322] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/21/2024] [Revised: 04/01/2025] [Accepted: 04/07/2025] [Indexed: 05/14/2025]  Open
5
Silver LW, Farquharson KA, Peel E, Gilbert MTP, Belov K, Morales HE, Hogg CJ. Temporal Loss of Genome-Wide and Immunogenetic Diversity in a Near-Extinct Parrot. Mol Ecol 2025;34:e17746. [PMID: 40130423 PMCID: PMC12010471 DOI: 10.1111/mec.17746] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/09/2024] [Revised: 02/14/2025] [Accepted: 03/13/2025] [Indexed: 03/26/2025]
6
Garcia-Erill G, Liu S, Le MD, Hurley MM, Nguyen HD, Nguyen DQ, Nguyen DH, Santander CG, Sánchez Barreiro F, Gomes Martins NF, Hanghøj K, Salleh FM, Ramos-Madrigal J, Wang X, Sinding MHS, Morales HE, Stæger FF, Wilkinson N, Meng G, Pečnerová P, Yang C, Rasmussen MS, Schubert M, Dunn RR, Moltke I, Zhang G, Chen L, Wang W, Cao TT, Nguyen HM, Siegismund HR, Albrechtsen A, Gilbert MTP, Heller R. Genomes of critically endangered saola are shaped by population structure and purging. Cell 2025:S0092-8674(25)00390-3. [PMID: 40328258 DOI: 10.1016/j.cell.2025.03.040] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/25/2024] [Revised: 12/20/2024] [Accepted: 03/25/2025] [Indexed: 05/08/2025]
7
More KD, Lebrasseur O, Garrido JL, Seguin-Orlando A, Discamps E, Estrada O, Tonasso-Calvière L, Chauvey L, Tressières G, Schiavinato S, Gibert M, Padula H, Chiavazza H, Fernández PM, Guardia NM, Borges C, Bertani S, Contreras-Mancilla J, Allccarima-Crisóstomo D, Fhon M, Barrey E, Charliquart L, Robbe E, de Noblet T, Zhumatayev R, Shakenov S, Vila E, Berthon R, Mashkour M, Khazaeli R, Nikgoftar A, Vahdati AA, Kosintsev P, Houle JL, Bayarsaikhan J, Wilczynski J, Moskal-Del Hoyo M, Nowak M, Taylor W, Bălășescu A, Dobrescu R, Benecke N, Arbuckle B, Steadman S, McMahon G, Šikanjić PR, Buric M, Vukičević TT, Alvarez N, Castel JC, Boudadi-Maligne M, Star B, Post-Melbye JR, Rødsrud CL, Stanton DWG, Charlton S, Mullin VE, Daly KG, Burgos NS, Pablos A, Dalen L, Bradley DG, Frantz L, Larson G, Orlando L. Validating a Target-Enrichment Design for Capturing Uniparental Haplotypes in Ancient Domesticated Animals. Mol Ecol Resour 2025:e14112. [PMID: 40202701 DOI: 10.1111/1755-0998.14112] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/06/2025] [Accepted: 03/20/2025] [Indexed: 04/10/2025]
8
De Cahsan B, Sandoval Velasco M, Westbury MV, Duchêne DA, Strander Sinding MH, Morales HE, Kalthoff DC, Barnes I, Brace S, Portela Miguez R, Roca AL, Greenwood AD, Johnson RN, Lott MJ, Gilbert MTP. Road to Extinction? Past and Present Population Structure and Genomic Diversity in the Koala. Mol Biol Evol 2025;42:msaf057. [PMID: 40129172 PMCID: PMC12014528 DOI: 10.1093/molbev/msaf057] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/07/2024] [Revised: 01/28/2025] [Accepted: 02/24/2025] [Indexed: 03/26/2025]  Open
9
Eriksen EF, Andrews AJ, Nielsen SV, Persson P, Malca E, Onar V, Aniceti V, Piquès G, Piattoni F, Fontani F, Wiech M, Ferter K, Kersten O, Ferrari G, Cariani A, Tinti F, Cilli E, Atmore LM, Star B. Five millennia of mitonuclear discordance in Atlantic bluefin tuna identified using ancient DNA. Heredity (Edinb) 2025;134:175-185. [PMID: 39920258 PMCID: PMC11977281 DOI: 10.1038/s41437-025-00745-1] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/24/2024] [Revised: 01/21/2025] [Accepted: 01/22/2025] [Indexed: 02/09/2025]  Open
10
Jensen EL, Marchisio C, Ochoa A, Gray R, Parra V, Miller JM, Çilingir FG, Caccone A. Synteny Enabled Upgrade of the Galapagos Giant Tortoise Genome Improves Inferences of Runs of Homozygosity. Ecol Evol 2025;15:e71358. [PMID: 40290375 PMCID: PMC12032190 DOI: 10.1002/ece3.71358] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/19/2024] [Revised: 03/26/2025] [Accepted: 04/15/2025] [Indexed: 04/30/2025]  Open
11
Kirkland C, Wang X, Canedo-Ribeiro C, Álvarez-González L, Weisz D, Mena A, St Leger J, Dudchenko O, Aiden EL, Ruiz-Herrera A, Heller R, King T, Farré M. Chromosome-level genomics and historical museum collections reveal new insights into the population structure and chromosome evolution of waterbuck. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2025:2025.03.19.644014. [PMID: 40166267 PMCID: PMC11956998 DOI: 10.1101/2025.03.19.644014] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 04/02/2025]
12
Lobo D, Morales HE, Van Oosterhout C, López-Bao JV, Silva P, Llaneza L, Pacheco C, Castro D, Hernández-Alonso G, Pacheco G, Archer J, Gilbert MTP, Ferrand N, Godinho R. Ancient dog introgression into the Iberian wolf genome may have facilitated adaptation to human-dominated landscapes. Genome Res 2025;35:432-445. [PMID: 39952679 PMCID: PMC11960463 DOI: 10.1101/gr.279093.124] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/22/2024] [Accepted: 02/06/2025] [Indexed: 02/17/2025]
13
Liu S, Gao Y, Long X, Li K, Gutang Q, Xie H, Wang J, Tian J, Liang B, Lin J, Liu W. A Possible More Precise Management Unit Delineation Based on Epigenomic Differentiation of a Long-Distance-Migratory Marine Fish Scomberomorus niphonius. Mol Ecol Resour 2025:e14103. [PMID: 40084530 DOI: 10.1111/1755-0998.14103] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/03/2024] [Revised: 02/22/2025] [Accepted: 03/05/2025] [Indexed: 03/16/2025]
14
Wilson J, Bieker VC, van Boheemen L, Connallon T, Martin MD, Battlay P, Hodgins KA. Copy number variation contributes to parallel local adaptation in an invasive plant. Proc Natl Acad Sci U S A 2025;122:e2413587122. [PMID: 40030023 PMCID: PMC11912486 DOI: 10.1073/pnas.2413587122] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/14/2024] [Accepted: 12/31/2024] [Indexed: 03/19/2025]  Open
15
Liu X, Milesi E, Fontsere C, Owens HL, Heinsohn R, Gilbert MTP, Crates R, Nogués-Bravo D, Morales HE. Time-lagged genomic erosion and future environmental risks in a bird on the brink of extinction. Proc Biol Sci 2025;292:20242480. [PMID: 40132633 PMCID: PMC11936686 DOI: 10.1098/rspb.2024.2480] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/15/2024] [Revised: 01/30/2025] [Accepted: 03/04/2025] [Indexed: 03/27/2025]  Open
16
Battlay P, Craig S, Putra AR, Monro K, De Silva NP, Wilson J, Bieker VC, Kabir S, Shamaya N, van Boheemen L, Rieseberg LH, Stinchcombe JR, Fournier-Level A, Martin MD, Hodgins KA. Rapid Parallel Adaptation in Distinct Invasions of Ambrosia Artemisiifolia Is Driven by Large-Effect Structural Variants. Mol Biol Evol 2025;42:msae270. [PMID: 39812008 PMCID: PMC11733498 DOI: 10.1093/molbev/msae270] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/24/2024] [Revised: 11/21/2024] [Accepted: 12/17/2024] [Indexed: 01/16/2025]  Open
17
Battilani D, Gargiulo R, Caniglia R, Fabbri E, Madrigal JR, Fontsere C, Ciucani MM, Gopalakrishnan S, Girardi M, Fracasso I, Mastroiaco M, Ciucci P, Vernesi C. Beyond population size: Whole-genome data reveal bottleneck legacies in the peninsular Italian wolf. J Hered 2025;116:10-23. [PMID: 39189963 DOI: 10.1093/jhered/esae041] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/15/2024] [Accepted: 08/15/2024] [Indexed: 08/28/2024]  Open
18
Bon C. [Paleoepigenetics: when DNA damages become epigenetic traces]. Med Sci (Paris) 2024;40:965-970. [PMID: 39705568 DOI: 10.1051/medsci/2024171] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/22/2024]  Open
19
Atmore LM, van der Jagt I, Boilard A, Häberle S, Blevis R, Dierickx K, Quinlan LM, Orton DC, Hufthammer AK, Barrett JH, Star B. The Once and Future Fish: Assessing a Millennium of Atlantic Herring Exploitation Through Mixed-Stock Analysis and Ancient DNA. GLOBAL CHANGE BIOLOGY 2024;30:e70010. [PMID: 39723543 DOI: 10.1111/gcb.70010] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/05/2024] [Revised: 11/22/2024] [Accepted: 12/09/2024] [Indexed: 12/28/2024]
20
Wang X, Pedersen CET, Athanasiadis G, Garcia-Erill G, Hanghøj K, Bertola LD, Rasmussen MS, Schubert M, Liu X, Li Z, Lin L, Balboa RF, Jørsboe E, Nursyifa C, Liu S, Muwanika V, Masembe C, Chen L, Wang W, Moltke I, Siegismund HR, Albrechtsen A, Heller R. Persistent Gene Flow Suggests an Absence of Reproductive Isolation in an African Antelope Speciation Model. Syst Biol 2024;73:979-994. [PMID: 39140829 PMCID: PMC11637686 DOI: 10.1093/sysbio/syae037] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/17/2023] [Revised: 03/22/2024] [Accepted: 08/04/2024] [Indexed: 08/15/2024]  Open
21
Zhur KV, Sharko FS, Leonova MV, Mey A, Prokhortchouk EB, Trifonov VA. Human DNA from the oldest Eneolithic cemetery in Nalchik points the spread of farming from the Caucasus to the Eastern European steppes. iScience 2024;27:110963. [PMID: 39569382 PMCID: PMC11576401 DOI: 10.1016/j.isci.2024.110963] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/19/2024] [Revised: 07/30/2024] [Accepted: 09/11/2024] [Indexed: 11/22/2024]  Open
22
Martínez-García L, Pulido A, Ferrari G, Hufthammer AK, Vedeler M, Hirons A, Kneale C, Barrett JH, Star B. Tracing 600 years of long-distance Atlantic cod trade in medieval and post-medieval Oslo using stable isotopes and ancient DNA. Proc Biol Sci 2024;291:20242019. [PMID: 39592000 PMCID: PMC11597396 DOI: 10.1098/rspb.2024.2019] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/05/2024] [Revised: 11/04/2024] [Accepted: 11/04/2024] [Indexed: 11/28/2024]  Open
23
Pan J, Liu X, Baca M, Calvière-Tonasso L, Schiavinato S, Chauvey L, Tressières G, Perdereau A, Aury JM, Oliveira PH, Wincker P, Abdykanova A, Arsuaga JL, Bayarsaikhan J, Belinskiy AB, Carbonell E, Davoudi H, Lira Garrido J, Gilbert AS, Hermes T, Warinner C, Kalmykov AA, Lordkipanidze D, Mackiewicz P, Mohaseb AF, Richter K, Sayfullaev N, Shapiro B, Shnaider S, Southon J, Stefaniak K, Summers GD, van Asperen EN, Vanishvili N, Hill EA, Kuznetsov P, Reinhold S, Hansen S, Mashkour M, Berthon R, Taylor WTT, Houle JL, Hekkala E, Popović D, Orlando L. Genome-wide population affinities and signatures of adaptation in hydruntines, sussemiones and Asian wild asses. Mol Ecol 2024;33:e17527. [PMID: 39279684 DOI: 10.1111/mec.17527] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/28/2023] [Revised: 06/08/2024] [Accepted: 09/03/2024] [Indexed: 09/18/2024]
24
Ruiz-Puerta EJ, Jarrett G, McCarthy ML, Pan SE, Keighley X, Aiken M, Zampirolo G, Loonen MJJE, Gotfredsen AB, Howse LR, Szpak P, Pálsson S, Rufolo S, Malmquist HJ, Desjardins SPA, Olsen MT, Jordan PD. Greenland Norse walrus exploitation deep into the Arctic. SCIENCE ADVANCES 2024;10:eadq4127. [PMID: 39331710 PMCID: PMC11430631 DOI: 10.1126/sciadv.adq4127] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/13/2024] [Accepted: 08/26/2024] [Indexed: 09/29/2024]
25
Sun Y, Lorenzen ED, Westbury MV. Late Pleistocene polar bear genomes reveal the timing of allele fixation in key genes associated with Arctic adaptation. BMC Genomics 2024;25:826. [PMID: 39278943 PMCID: PMC11403954 DOI: 10.1186/s12864-024-10617-3] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/30/2023] [Accepted: 07/12/2024] [Indexed: 09/18/2024]  Open
26
Slimak L, Vimala T, Seguin-Orlando A, Metz L, Zanolli C, Joannes-Boyau R, Frouin M, Arnold LJ, Demuro M, Devièse T, Comeskey D, Buckley M, Camus H, Muth X, Lewis JE, Bocherens H, Yvorra P, Tenailleau C, Duployer B, Coqueugniot H, Dutour O, Higham T, Sikora M. Long genetic and social isolation in Neanderthals before their extinction. CELL GENOMICS 2024;4:100593. [PMID: 39265525 PMCID: PMC11480857 DOI: 10.1016/j.xgen.2024.100593] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/04/2023] [Revised: 11/23/2023] [Accepted: 06/05/2024] [Indexed: 09/14/2024]
27
Skovrind M, Louis M, Ferguson SH, Glazov DM, Litovka DI, Loseto L, Meschersky IG, Miller MM, Petr M, Postma L, Rozhnov VV, Scott M, Westbury MV, Szpak P, Friesen TM, Lorenzen ED. Elucidating the sustainability of 700 y of Inuvialuit beluga whale hunting in the Mackenzie River Delta, Northwest Territories, Canada. Proc Natl Acad Sci U S A 2024;121:e2405993121. [PMID: 39136992 PMCID: PMC11348011 DOI: 10.1073/pnas.2405993121] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/02/2024] [Accepted: 07/08/2024] [Indexed: 08/29/2024]  Open
28
Przelomska NAS, Diaz RA, Ávila FA, Ballen GA, Cortés-B R, Kistler L, Chitwood DH, Charitonidou M, Renner SS, Pérez-Escobar OA, Antonelli A. Morphometrics and Phylogenomics of Coca (Erythroxylum spp.) Illuminate Its Reticulate Evolution, With Implications for Taxonomy. Mol Biol Evol 2024;41:msae114. [PMID: 38982580 PMCID: PMC11233275 DOI: 10.1093/molbev/msae114] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/08/2023] [Revised: 05/01/2024] [Accepted: 05/10/2024] [Indexed: 07/11/2024]  Open
29
Librado P, Tressières G, Chauvey L, Fages A, Khan N, Schiavinato S, Calvière-Tonasso L, Kusliy MA, Gaunitz C, Liu X, Wagner S, Der Sarkissian C, Seguin-Orlando A, Perdereau A, Aury JM, Southon J, Shapiro B, Bouchez O, Donnadieu C, Collin YRH, Gregersen KM, Jessen MD, Christensen K, Claudi-Hansen L, Pruvost M, Pucher E, Vulic H, Novak M, Rimpf A, Turk P, Reiter S, Brem G, Schwall C, Barrey É, Robert C, Degueurce C, Horwitz LK, Klassen L, Rasmussen U, Kveiborg J, Johannsen NN, Makowiecki D, Makarowicz P, Szeliga M, Ilchyshyn V, Rud V, Romaniszyn J, Mullin VE, Verdugo M, Bradley DG, Cardoso JL, Valente MJ, Telles Antunes M, Ameen C, Thomas R, Ludwig A, Marzullo M, Prato O, Bagnasco Gianni G, Tecchiati U, Granado J, Schlumbaum A, Deschler-Erb S, Mráz MS, Boulbes N, Gardeisen A, Mayer C, Döhle HJ, Vicze M, Kosintsev PA, Kyselý R, Peške L, O'Connor T, Ananyevskaya E, Shevnina I, Logvin A, Kovalev AA, Iderkhangai TO, Sablin MV, Dashkovskiy PK, Graphodatsky AS, Merts I, Merts V, Kasparov AK, Pitulko VV, Onar V, Öztan A, Arbuckle BS, McColl H, Renaud G, Khaskhanov R, Demidenko S, Kadieva A, Atabiev B, Sundqvist M, Lindgren G, López-Cachero FJ, Albizuri S, Trbojević Vukičević T, Rapan Papeša A, et alLibrado P, Tressières G, Chauvey L, Fages A, Khan N, Schiavinato S, Calvière-Tonasso L, Kusliy MA, Gaunitz C, Liu X, Wagner S, Der Sarkissian C, Seguin-Orlando A, Perdereau A, Aury JM, Southon J, Shapiro B, Bouchez O, Donnadieu C, Collin YRH, Gregersen KM, Jessen MD, Christensen K, Claudi-Hansen L, Pruvost M, Pucher E, Vulic H, Novak M, Rimpf A, Turk P, Reiter S, Brem G, Schwall C, Barrey É, Robert C, Degueurce C, Horwitz LK, Klassen L, Rasmussen U, Kveiborg J, Johannsen NN, Makowiecki D, Makarowicz P, Szeliga M, Ilchyshyn V, Rud V, Romaniszyn J, Mullin VE, Verdugo M, Bradley DG, Cardoso JL, Valente MJ, Telles Antunes M, Ameen C, Thomas R, Ludwig A, Marzullo M, Prato O, Bagnasco Gianni G, Tecchiati U, Granado J, Schlumbaum A, Deschler-Erb S, Mráz MS, Boulbes N, Gardeisen A, Mayer C, Döhle HJ, Vicze M, Kosintsev PA, Kyselý R, Peške L, O'Connor T, Ananyevskaya E, Shevnina I, Logvin A, Kovalev AA, Iderkhangai TO, Sablin MV, Dashkovskiy PK, Graphodatsky AS, Merts I, Merts V, Kasparov AK, Pitulko VV, Onar V, Öztan A, Arbuckle BS, McColl H, Renaud G, Khaskhanov R, Demidenko S, Kadieva A, Atabiev B, Sundqvist M, Lindgren G, López-Cachero FJ, Albizuri S, Trbojević Vukičević T, Rapan Papeša A, Burić M, Rajić Šikanjić P, Weinstock J, Asensio Vilaró D, Codina F, García Dalmau C, Morer de Llorens J, Pou J, de Prado G, Sanmartí J, Kallala N, Torres JR, Maraoui-Telmini B, Belarte Franco MC, Valenzuela-Lamas S, Zazzo A, Lepetz S, Duchesne S, Alexeev A, Bayarsaikhan J, Houle JL, Bayarkhuu N, Turbat T, Crubézy É, Shingiray I, Mashkour M, Berezina NY, Korobov DS, Belinskiy A, Kalmykov A, Demoule JP, Reinhold S, Hansen S, Wallner B, Roslyakova N, Kuznetsov PF, Tishkin AA, Wincker P, Kanne K, Outram A, Orlando L. Widespread horse-based mobility arose around 2200 BCE in Eurasia. Nature 2024;631:819-825. [PMID: 38843826 PMCID: PMC11269178 DOI: 10.1038/s41586-024-07597-5] [Show More Authors] [Citation(s) in RCA: 9] [Impact Index Per Article: 9.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/17/2023] [Accepted: 05/23/2024] [Indexed: 07/19/2024]
30
Cavill EL, Morales HE, Sun X, Westbury MV, van Oosterhout C, Accouche W, Zora A, Schulze MJ, Shah N, Adam P, Brooke MDL, Sweet P, Gopalakrishnan S, Gilbert MTP. When birds of a feather flock together: Severe genomic erosion and the implications for genetic rescue in an endangered island passerine. Evol Appl 2024;17:e13739. [PMID: 38948538 PMCID: PMC11212007 DOI: 10.1111/eva.13739] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/30/2023] [Revised: 05/22/2024] [Accepted: 06/04/2024] [Indexed: 07/02/2024]  Open
31
Zhu S, Zhang N, Zhang J, Shao X, Guo Y, Cai D. Ancient Mitochondrial Genomes Provide New Clues in the History of the Akhal-Teke Horse in China. Genes (Basel) 2024;15:790. [PMID: 38927726 PMCID: PMC11203007 DOI: 10.3390/genes15060790] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/14/2024] [Revised: 06/11/2024] [Accepted: 06/13/2024] [Indexed: 06/28/2024]  Open
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Rayo E, Ulrich GF, Zemp N, Greeff M, Schuenemann VJ, Widmer A, Fischer MC. Minimally destructive hDNA extraction method for retrospective genetics of pinned historical Lepidoptera specimens. Sci Rep 2024;14:12875. [PMID: 38834639 DOI: 10.1038/s41598-024-63587-7] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/29/2024] [Accepted: 05/30/2024] [Indexed: 06/06/2024]  Open
33
Fegraeus K, Rosengren MK, Naboulsi R, Orlando L, Åbrink M, Jouni A, Velie BD, Raine A, Egner B, Mattsson CM, Lång K, Zhigulev A, Björck HM, Franco-Cereceda A, Eriksson P, Andersson G, Sahlén P, Meadows JRS, Lindgren G. An endothelial regulatory module links blood pressure regulation with elite athletic performance. PLoS Genet 2024;20:e1011285. [PMID: 38885195 PMCID: PMC11182536 DOI: 10.1371/journal.pgen.1011285] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/10/2023] [Accepted: 05/02/2024] [Indexed: 06/20/2024]  Open
34
Borry M, Forsythe A, Andrades Valtueña A, Hübner A, Ibrahim A, Quagliariello A, White AE, Kocher A, Vågene ÅJ, Bartholdy BP, Spurīte D, Ponce-Soto GY, Neumann G, Huang IT, Light I, Velsko IM, Jackson I, Frangenberg J, Serrano JG, Fumey J, Özdoğan KT, Blevins KE, Daly KG, Lopopolo M, Moraitou M, Michel M, van Os M, Bravo-Lopez MJ, Sarhan MS, Dagtas ND, Oskolkov N, Smith OS, Lebrasseur O, Rozwalak P, Eisenhofer R, Wasef S, Ramachandran SL, Vanghi V, Warinner C, Fellows Yates JA. Facilitating accessible, rapid, and appropriate processing of ancient metagenomic data with AMDirT. F1000Res 2024;12:926. [PMID: 39262445 PMCID: PMC11387932 DOI: 10.12688/f1000research.134798.2] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Accepted: 05/07/2024] [Indexed: 09/13/2024]  Open
35
Martin-Roy R, Thyrring J, Mata X, Bangsgaard P, Bennike O, Christiansen G, Funder S, Gotfredsen AB, Gregersen KM, Hansen CH, Ilsøe PC, Klassen L, Kristensen IK, Ravnholt GB, Marin F, Der Sarkissian C. Advancing responsible genomic analyses of ancient mollusc shells. PLoS One 2024;19:e0302646. [PMID: 38709766 PMCID: PMC11073703 DOI: 10.1371/journal.pone.0302646] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/12/2024] [Accepted: 04/09/2024] [Indexed: 05/08/2024]  Open
36
Hempel E, Faith JT, Preick M, de Jager D, Barish S, Hartmann S, Grau JH, Moodley Y, Gedman G, Pirovich KM, Bibi F, Kalthoff DC, Bocklandt S, Lamm B, Dalén L, Westbury MV, Hofreiter M. Colonial-driven extinction of the blue antelope despite genomic adaptation to low population size. Curr Biol 2024;34:2020-2029.e6. [PMID: 38614080 DOI: 10.1016/j.cub.2024.03.051] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/20/2023] [Revised: 02/09/2024] [Accepted: 03/25/2024] [Indexed: 04/15/2024]
37
Liu X, Lin L, Sinding MHS, Bertola LD, Hanghøj K, Quinn L, Garcia-Erill G, Rasmussen MS, Schubert M, Pečnerová P, Balboa RF, Li Z, Heaton MP, Smith TPL, Pinto RR, Wang X, Kuja J, Brüniche-Olsen A, Meisner J, Santander CG, Ogutu JO, Masembe C, da Fonseca RR, Muwanika V, Siegismund HR, Albrechtsen A, Moltke I, Heller R. Introgression and disruption of migration routes have shaped the genetic integrity of wildebeest populations. Nat Commun 2024;15:2921. [PMID: 38609362 PMCID: PMC11014984 DOI: 10.1038/s41467-024-47015-y] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/31/2023] [Accepted: 03/11/2024] [Indexed: 04/14/2024]  Open
38
Bertola LD, Quinn L, Hanghøj K, Garcia-Erill G, Rasmussen MS, Balboa RF, Meisner J, Bøggild T, Wang X, Lin L, Nursyifa C, Liu X, Li Z, Chege M, Moodley Y, Brüniche-Olsen A, Kuja J, Schubert M, Agaba M, Santander CG, Sinding MHS, Muwanika V, Masembe C, Siegismund HR, Moltke I, Albrechtsen A, Heller R. Giraffe lineages are shaped by major ancient admixture events. Curr Biol 2024;34:1576-1586.e5. [PMID: 38479386 DOI: 10.1016/j.cub.2024.02.051] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/11/2023] [Revised: 09/29/2023] [Accepted: 02/21/2024] [Indexed: 04/11/2024]
39
Sosale MS, Roelke-Parker M, Machange GA, Edwards CW, Figueiró HV, Koepfli KP. The complete mitochondrial genome of Meller's mongoose (Rhynchogale melleri). Mitochondrial DNA B Resour 2024;9:432-436. [PMID: 38586507 PMCID: PMC10993741 DOI: 10.1080/23802359.2024.2333567] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/08/2023] [Accepted: 03/15/2024] [Indexed: 04/09/2024]  Open
40
Cobb L, de Muinck E, Kollias S, Skage M, Gilfillan GD, Sydenham MAK, Qiao SW, Star B. High-throughput sequencing of insect specimens with sub-optimal DNA preservation using a practical, plate-based Illumina-compatible Tn5 transposase library preparation method. PLoS One 2024;19:e0300865. [PMID: 38517905 PMCID: PMC10959394 DOI: 10.1371/journal.pone.0300865] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/11/2023] [Accepted: 03/06/2024] [Indexed: 03/24/2024]  Open
41
Kellner FL, Le Moullec M, Ellegaard MR, Rosvold J, Peeters B, Burnett HA, Pedersen ÅØ, Brealey JC, Dussex N, Bieker VC, Hansen BB, Martin MD. A palaeogenomic investigation of overharvest implications in an endemic wild reindeer subspecies. Mol Ecol 2024;33:e17274. [PMID: 38279681 DOI: 10.1111/mec.17274] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/24/2023] [Revised: 12/11/2023] [Accepted: 01/09/2024] [Indexed: 01/28/2024]
42
Lin C, Lu Y, Liu S, Wang Z, Yao L, Yin Y, Jiao L. Retrieving complete plastid genomes of endangered Guibourtia timber using hybridization capture for forensic identification and phylogenetic analysis. Forensic Sci Int Genet 2024;69:103006. [PMID: 38171223 DOI: 10.1016/j.fsigen.2023.103006] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/30/2023] [Revised: 11/25/2023] [Accepted: 12/21/2023] [Indexed: 01/05/2024]
43
Verry AJF, Mas-Carrió E, Gibb GC, Dutoit L, Robertson BC, Waters JM, Rawlence NJ. Ancient mitochondrial genomes unveil the origins and evolutionary history of New Zealand's enigmatic takahē and moho. Mol Ecol 2024;33:e17227. [PMID: 38018770 DOI: 10.1111/mec.17227] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/02/2023] [Revised: 11/05/2023] [Accepted: 11/17/2023] [Indexed: 11/30/2023]
44
Gavriil M, Proietto M, Paczia N, Ginolhac A, Halder R, Valceschini E, Sauter T, Linster CL, Sinkkonen L. 2-Hydroxyglutarate modulates histone methylation at specific loci and alters gene expression via Rph1 inhibition. Life Sci Alliance 2024;7:e202302333. [PMID: 38011998 PMCID: PMC10681907 DOI: 10.26508/lsa.202302333] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/23/2023] [Revised: 11/21/2023] [Accepted: 11/21/2023] [Indexed: 11/29/2023]  Open
45
Wagner S, Seguin-Orlando A, Leplé JC, Leroy T, Lalanne C, Labadie K, Aury JM, Poirier S, Wincker P, Plomion C, Kremer A, Orlando L. Tracking population structure and phenology through time using ancient genomes from waterlogged white oak wood. Mol Ecol 2024;33:e16859. [PMID: 36748324 PMCID: PMC7615563 DOI: 10.1111/mec.16859] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/24/2022] [Revised: 12/08/2022] [Accepted: 01/16/2023] [Indexed: 02/08/2023]
46
Segawa T, Rey-Iglesia A, Lorenzen ED, Westbury MV. The origins and diversification of Holarctic brown bear populations inferred from genomes of past and present populations. Proc Biol Sci 2024;291:20232411. [PMID: 38264778 PMCID: PMC10806438 DOI: 10.1098/rspb.2023.2411] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/12/2023] [Accepted: 12/20/2023] [Indexed: 01/25/2024]  Open
47
Lebrasseur O, More KD, Orlando L. Equine herpesvirus 4 infected domestic horses associated with Sintashta spoke-wheeled chariots around 4,000 years ago. Virus Evol 2024;10:vead087. [PMID: 38465241 PMCID: PMC10924538 DOI: 10.1093/ve/vead087] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/28/2023] [Revised: 11/27/2023] [Accepted: 01/11/2024] [Indexed: 03/12/2024]  Open
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Swain T, Pflueger C, Freytag S, Poppe D, Pflueger J, Nguyen T, Li J, Lister R. A modular dCas9-based recruitment platform for combinatorial epigenome editing. Nucleic Acids Res 2024;52:474-491. [PMID: 38000387 PMCID: PMC10783489 DOI: 10.1093/nar/gkad1108] [Citation(s) in RCA: 7] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/05/2022] [Revised: 09/28/2023] [Accepted: 11/02/2023] [Indexed: 11/26/2023]  Open
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Bennasar-Figueras A. The Natural and Clinical History of Plague: From the Ancient Pandemics to Modern Insights. Microorganisms 2024;12:146. [PMID: 38257973 PMCID: PMC10818976 DOI: 10.3390/microorganisms12010146] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/19/2023] [Revised: 01/02/2024] [Accepted: 01/08/2024] [Indexed: 01/24/2024]  Open
50
Balboa RF, Bertola LD, Brüniche-Olsen A, Rasmussen MS, Liu X, Besnard G, Salmona J, Santander CG, He S, Zinner D, Pedrono M, Muwanika V, Masembe C, Schubert M, Kuja J, Quinn L, Garcia-Erill G, Stæger FF, Rakotoarivony R, Henrique M, Lin L, Wang X, Heaton MP, Smith TPL, Hanghøj K, Sinding MHS, Atickem A, Chikhi L, Roos C, Gaubert P, Siegismund HR, Moltke I, Albrechtsen A, Heller R. African bushpigs exhibit porous species boundaries and appeared in Madagascar concurrently with human arrival. Nat Commun 2024;15:172. [PMID: 38172616 PMCID: PMC10764920 DOI: 10.1038/s41467-023-44105-1] [Citation(s) in RCA: 5] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/23/2023] [Accepted: 11/30/2023] [Indexed: 01/05/2024]  Open
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