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For: de Manuel M, Kuhlwilm M, Frandsen P, Sousa VC, Desai T, Prado-Martinez J, Hernandez-Rodriguez J, Dupanloup I, Lao O, Hallast P, Schmidt JM, Heredia-Genestar JM, Benazzo A, Barbujani G, Peter BM, Kuderna LFK, Casals F, Angedakin S, Arandjelovic M, Boesch C, Kühl H, Vigilant L, Langergraber K, Novembre J, Gut M, Gut I, Navarro A, Carlsen F, Andrés AM, Siegismund HR, Scally A, Excoffier L, Tyler-Smith C, Castellano S, Xue Y, Hvilsom C, Marques-Bonet T. Chimpanzee genomic diversity reveals ancient admixture with bonobos. Science 2016;354:477-481. [PMID: 27789843 DOI: 10.1126/science.aag2602] [Citation(s) in RCA: 166] [Impact Index Per Article: 18.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/02/2016] [Accepted: 09/09/2016] [Indexed: 12/13/2022]
Number Cited by Other Article(s)
1
Brooks J, Clay Z, Dufour V, Fedurek P, Girard-Buttoz C, Yamamoto S. Collective Acoustics in Pan: Conserved Roots in the Evolution of Human Musicality. Am J Primatol 2025;87:e70048. [PMID: 40434096 DOI: 10.1002/ajp.70048] [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: 10/08/2024] [Revised: 03/14/2025] [Accepted: 05/18/2025] [Indexed: 05/29/2025]
2
Yoo D, Rhie A, Hebbar P, Antonacci F, Logsdon GA, Solar SJ, Antipov D, Pickett BD, Safonova Y, Montinaro F, Luo Y, Malukiewicz J, Storer JM, Lin J, Sequeira AN, Mangan RJ, Hickey G, Monfort Anez G, Balachandran P, Bankevich A, Beck CR, Biddanda A, Borchers M, Bouffard GG, Brannan E, Brooks SY, Carbone L, Carrel L, Chan AP, Crawford J, Diekhans M, Engelbrecht E, Feschotte C, Formenti G, Garcia GH, de Gennaro L, Gilbert D, Green RE, Guarracino A, Gupta I, Haddad D, Han J, Harris RS, Hartley GA, Harvey WT, Hiller M, Hoekzema K, Houck ML, Jeong H, Kamali K, Kellis M, Kille B, Lee C, Lee Y, Lees W, Lewis AP, Li Q, Loftus M, Loh YHE, Loucks H, Ma J, Mao Y, Martinez JFI, Masterson P, McCoy RC, McGrath B, McKinney S, Meyer BS, Miga KH, Mohanty SK, Munson KM, Pal K, Pennell M, Pevzner PA, Porubsky D, Potapova T, Ringeling FR, Rocha JL, Ryder OA, Sacco S, Saha S, Sasaki T, Schatz MC, Schork NJ, Shanks C, Smeds L, Son DR, Steiner C, Sweeten AP, Tassia MG, Thibaud-Nissen F, Torres-González E, Trivedi M, Wei W, Wertz J, Yang M, Zhang P, Zhang S, Zhang Y, Zhang Z, et alYoo D, Rhie A, Hebbar P, Antonacci F, Logsdon GA, Solar SJ, Antipov D, Pickett BD, Safonova Y, Montinaro F, Luo Y, Malukiewicz J, Storer JM, Lin J, Sequeira AN, Mangan RJ, Hickey G, Monfort Anez G, Balachandran P, Bankevich A, Beck CR, Biddanda A, Borchers M, Bouffard GG, Brannan E, Brooks SY, Carbone L, Carrel L, Chan AP, Crawford J, Diekhans M, Engelbrecht E, Feschotte C, Formenti G, Garcia GH, de Gennaro L, Gilbert D, Green RE, Guarracino A, Gupta I, Haddad D, Han J, Harris RS, Hartley GA, Harvey WT, Hiller M, Hoekzema K, Houck ML, Jeong H, Kamali K, Kellis M, Kille B, Lee C, Lee Y, Lees W, Lewis AP, Li Q, Loftus M, Loh YHE, Loucks H, Ma J, Mao Y, Martinez JFI, Masterson P, McCoy RC, McGrath B, McKinney S, Meyer BS, Miga KH, Mohanty SK, Munson KM, Pal K, Pennell M, Pevzner PA, Porubsky D, Potapova T, Ringeling FR, Rocha JL, Ryder OA, Sacco S, Saha S, Sasaki T, Schatz MC, Schork NJ, Shanks C, Smeds L, Son DR, Steiner C, Sweeten AP, Tassia MG, Thibaud-Nissen F, Torres-González E, Trivedi M, Wei W, Wertz J, Yang M, Zhang P, Zhang S, Zhang Y, Zhang Z, Zhao SA, Zhu Y, Jarvis ED, Gerton JL, Rivas-González I, Paten B, Szpiech ZA, Huber CD, Lenz TL, Konkel MK, Yi SV, Canzar S, Watson CT, Sudmant PH, Molloy E, Garrison E, Lowe CB, Ventura M, O'Neill RJ, Koren S, Makova KD, Phillippy AM, Eichler EE. Complete sequencing of ape genomes. Nature 2025;641:401-418. [PMID: 40205052 PMCID: PMC12058530 DOI: 10.1038/s41586-025-08816-3] [Show More Authors] [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: 07/31/2024] [Accepted: 02/19/2025] [Indexed: 04/11/2025]
3
Cousins T, Scally A, Durbin R. A structured coalescent model reveals deep ancestral structure shared by all modern humans. Nat Genet 2025;57:856-864. [PMID: 40102687 PMCID: PMC11985351 DOI: 10.1038/s41588-025-02117-1] [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: 03/24/2024] [Accepted: 02/05/2025] [Indexed: 03/20/2025]
4
Bisschop G, Kelleher J, Ralph P. Likelihoods for a general class of ARGs under the SMC. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2025:2025.02.24.639977. [PMID: 40060524 PMCID: PMC11888268 DOI: 10.1101/2025.02.24.639977] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Indexed: 03/22/2025]
5
Mendes FK, Bouckaert R, Carvalho LM, Drummond AJ. How to Validate a Bayesian Evolutionary Model. Syst Biol 2025;74:158-175. [PMID: 39506375 PMCID: PMC11809579 DOI: 10.1093/sysbio/syae064] [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: 03/26/2024] [Revised: 10/21/2024] [Accepted: 11/03/2024] [Indexed: 11/08/2024]  Open
6
Fong-Zazueta R, Krueger J, Alba DM, Aymerich X, Beck RMD, Cappellini E, Carrillo-Martin G, Cirilli O, Clark N, Cornejo OE, Farh KKH, Ferrández-Peral L, Juan D, Kelley JL, Kuderna LFK, Little J, Orkin JD, Paterson RS, Pawar H, Marques-Bonet T, Lizano E. Phylogenetic Signal in Primate Tooth Enamel Proteins and its Relevance for Paleoproteomics. Genome Biol Evol 2025;17:evaf007. [PMID: 39834226 PMCID: PMC11878541 DOI: 10.1093/gbe/evaf007] [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: 03/05/2024] [Revised: 12/17/2024] [Accepted: 01/10/2025] [Indexed: 01/22/2025]  Open
7
Hayakawa T, Kishida T, Go Y, Inoue E, Kawaguchi E, Aizu T, Ishizaki H, Toyoda A, Fujiyama A, Matsuzawa T, Hashimoto C, Furuichi T, Agata K. Genome-scale evolution in local populations of wild chimpanzees. Sci Rep 2025;15:548. [PMID: 39747985 PMCID: PMC11696052 DOI: 10.1038/s41598-024-84163-z] [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: 07/25/2024] [Accepted: 12/20/2024] [Indexed: 01/04/2025]  Open
8
Zhu Z, Han C, Huang S. New insights shed light on the enigma of genetic diversity and species complexity. SCIENCE CHINA. LIFE SCIENCES 2024;67:2774-2776. [PMID: 39167323 DOI: 10.1007/s11427-023-2610-2] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/09/2023] [Accepted: 05/04/2024] [Indexed: 08/23/2024]
9
Gunasekaram C, Battiston F, Sadekar O, Padilla-Iglesias C, van Noordwijk MA, Furrer R, Manica A, Bertranpetit J, Whiten A, van Schaik CP, Vinicius L, Migliano AB. Population connectivity shapes the distribution and complexity of chimpanzee cumulative culture. Science 2024;386:920-925. [PMID: 39571020 DOI: 10.1126/science.adk3381] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/28/2023] [Accepted: 09/23/2024] [Indexed: 04/18/2025]
10
Han S, de Filippo C, Parra G, Meneu JR, Laurent R, Frandsen P, Hvilsom C, Gronau I, Marques-Bonet T, Kuhlwilm M, Andrés AM. Deep genetic substructure within bonobos. Curr Biol 2024;34:5341-5348.e3. [PMID: 39413789 DOI: 10.1016/j.cub.2024.09.043] [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: 04/08/2024] [Revised: 07/07/2024] [Accepted: 09/17/2024] [Indexed: 10/18/2024]
11
Brand CM, Kuang S, Gilbertson EN, McArthur E, Pollard KS, Webster TH, Capra JA. Sequence-Based Machine Learning Reveals 3D Genome Differences between Bonobos and Chimpanzees. Genome Biol Evol 2024;16:evae210. [PMID: 39382451 PMCID: PMC11579661 DOI: 10.1093/gbe/evae210] [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: 04/30/2024] [Revised: 09/04/2024] [Accepted: 09/17/2024] [Indexed: 10/10/2024]  Open
12
Hermosilla-Albala N, Silva FE, Cuadros-Espinoza S, Fontsere C, Valenzuela-Seba A, Pawar H, Gut M, Kelley JL, Ruibal-Puertas S, Alentorn-Moron P, Faella A, Lizano E, Farias I, Hrbek T, Valsecchi J, Gut IG, Rogers J, Farh KKH, Kuderna LFK, Marques-Bonet T, Boubli JP. Whole genomes of Amazonian uakari monkeys reveal complex connectivity and fast differentiation driven by high environmental dynamism. Commun Biol 2024;7:1283. [PMID: 39379612 PMCID: PMC11461705 DOI: 10.1038/s42003-024-06901-3] [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: 10/02/2023] [Accepted: 09/16/2024] [Indexed: 10/10/2024]  Open
13
Yang Z, Deng M, Ren L, Fan Z, Yang S, Liu S, Ren X, Gao J, Cheng B, Xia J. Pyroptosis of oral keratinocyte contributes to energy metabolic reprogramming of T cells in oral lichen planus via OPA1-mediated mitochondrial fusion. Cell Death Discov 2024;10:408. [PMID: 39289349 PMCID: PMC11408637 DOI: 10.1038/s41420-024-02174-1] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/22/2024] [Revised: 09/03/2024] [Accepted: 09/05/2024] [Indexed: 09/19/2024]  Open
14
Brooks J, van Heijst K, Epping A, Lee SH, Niksarli A, Pope A, Clay Z, Kret ME, Taglialatela J, Yamamoto S. Increased alertness and moderate ingroup cohesion in bonobos' response to outgroup cues. PLoS One 2024;19:e0307975. [PMID: 39167568 PMCID: PMC11338468 DOI: 10.1371/journal.pone.0307975] [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: 10/16/2023] [Accepted: 07/15/2024] [Indexed: 08/23/2024]  Open
15
Langdon QK, Groh JS, Aguillon SM, Powell DL, Gunn T, Payne C, Baczenas JJ, Donny A, Dodge TO, Du K, Schartl M, Ríos-Cárdenas O, Gutiérrez-Rodríguez C, Morris M, Schumer M. Swordtail fish hybrids reveal that genome evolution is surprisingly predictable after initial hybridization. PLoS Biol 2024;22:e3002742. [PMID: 39186811 PMCID: PMC11379403 DOI: 10.1371/journal.pbio.3002742] [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: 12/30/2023] [Revised: 09/06/2024] [Accepted: 07/09/2024] [Indexed: 08/28/2024]  Open
16
Ostridge HJ, Fontsere C, Lizano E, Soto DC, Schmidt JM, Saxena V, Alvarez-Estape M, Barratt CD, Gratton P, Bocksberger G, Lester JD, Dieguez P, Agbor A, Angedakin S, Assumang AK, Bailey E, Barubiyo D, Bessone M, Brazzola G, Chancellor R, Cohen H, Coupland C, Danquah E, Deschner T, Dotras L, Dupain J, Egbe VE, Granjon AC, Head J, Hedwig D, Hermans V, Hernandez-Aguilar RA, Jeffery KJ, Jones S, Junker J, Kadam P, Kaiser M, Kalan AK, Kambere M, Kienast I, Kujirakwinja D, Langergraber KE, Lapuente J, Larson B, Laudisoit A, Lee KC, Llana M, Maretti G, Martín R, Meier A, Morgan D, Neil E, Nicholl S, Nixon S, Normand E, Orbell C, Ormsby LJ, Orume R, Pacheco L, Preece J, Regnaut S, Robbins MM, Rundus A, Sanz C, Sciaky L, Sommer V, Stewart FA, Tagg N, Tédonzong LR, van Schijndel J, Vendras E, Wessling EG, Willie J, Wittig RM, Yuh YG, Yurkiw K, Vigilant L, Piel A, Boesch C, Kühl HS, Dennis MY, Marques-Bonet T, Arandjelovic M, Andrés AM. Local genetic adaptation to habitat in wild chimpanzees. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2024:2024.07.09.601734. [PMID: 39026872 PMCID: PMC11257515 DOI: 10.1101/2024.07.09.601734] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 07/20/2024]
17
Makova KD, Pickett BD, Harris RS, Hartley GA, Cechova M, Pal K, Nurk S, Yoo D, Li Q, Hebbar P, McGrath BC, Antonacci F, Aubel M, Biddanda A, Borchers M, Bornberg-Bauer E, Bouffard GG, Brooks SY, Carbone L, Carrel L, Carroll A, Chang PC, Chin CS, Cook DE, Craig SJC, de Gennaro L, Diekhans M, Dutra A, Garcia GH, Grady PGS, Green RE, Haddad D, Hallast P, Harvey WT, Hickey G, Hillis DA, Hoyt SJ, Jeong H, Kamali K, Pond SLK, LaPolice TM, Lee C, Lewis AP, Loh YHE, Masterson P, McGarvey KM, McCoy RC, Medvedev P, Miga KH, Munson KM, Pak E, Paten B, Pinto BJ, Potapova T, Rhie A, Rocha JL, Ryabov F, Ryder OA, Sacco S, Shafin K, Shepelev VA, Slon V, Solar SJ, Storer JM, Sudmant PH, Sweetalana, Sweeten A, Tassia MG, Thibaud-Nissen F, Ventura M, Wilson MA, Young AC, Zeng H, Zhang X, Szpiech ZA, Huber CD, Gerton JL, Yi SV, Schatz MC, Alexandrov IA, Koren S, O'Neill RJ, Eichler EE, Phillippy AM. The complete sequence and comparative analysis of ape sex chromosomes. Nature 2024;630:401-411. [PMID: 38811727 PMCID: PMC11168930 DOI: 10.1038/s41586-024-07473-2] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/17/2023] [Accepted: 04/26/2024] [Indexed: 05/31/2024]
18
Sekhavati Y, Strait D. Estimating ancestral ranges and biogeographical processes in early hominins. J Hum Evol 2024;191:103547. [PMID: 38781711 DOI: 10.1016/j.jhevol.2024.103547] [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: 12/01/2022] [Revised: 05/05/2024] [Accepted: 05/06/2024] [Indexed: 05/25/2024]
19
Yee SW, Ferrández-Peral L, Alentorn-Moron P, Fontsere C, Ceylan M, Koleske ML, Handin N, Artegoitia VM, Lara G, Chien HC, Zhou X, Dainat J, Zalevsky A, Sali A, Brand CM, Wolfreys FD, Yang J, Gestwicki JE, Capra JA, Artursson P, Newman JW, Marquès-Bonet T, Giacomini KM. Illuminating the function of the orphan transporter, SLC22A10, in humans and other primates. Nat Commun 2024;15:4380. [PMID: 38782905 PMCID: PMC11116522 DOI: 10.1038/s41467-024-48569-7] [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: 08/14/2023] [Accepted: 05/06/2024] [Indexed: 05/25/2024]  Open
20
Silk JB. Animal behavior: A tale of two apes. Curr Biol 2024;34:R353-R355. [PMID: 38714164 DOI: 10.1016/j.cub.2024.03.056] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 05/09/2024]
21
Ortego J, Muñoz‐Fuentes V, López‐Luque R, Ball AD, Ghazali M, Abed SA, Salim MA, Green AJ. Demographic and conservation genomic assessment of the threatened marbled teal (Marmaronetta angustirostris). Evol Appl 2024;17:e13639. [PMID: 38721592 PMCID: PMC11077658 DOI: 10.1111/eva.13639] [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: 06/22/2023] [Revised: 12/14/2023] [Accepted: 12/15/2023] [Indexed: 01/06/2025]  Open
22
Foley RA, Mirazón Lahr M. Ghosts of extinct apes: genomic insights into African hominid evolution. Trends Ecol Evol 2024;39:456-466. [PMID: 38302324 DOI: 10.1016/j.tree.2023.12.009] [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: 04/04/2023] [Revised: 12/13/2023] [Accepted: 12/22/2023] [Indexed: 02/03/2024]
23
Mitani JC, Abwe E, Campbell G, Giles-Vernick T, Goldberg T, McLennan MR, Preuschoft S, Supriatna J, Marshall AJ. Future coexistence with great apes will require major changes to policy and practice. Nat Hum Behav 2024;8:632-643. [PMID: 38374442 DOI: 10.1038/s41562-024-01830-x] [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: 04/19/2023] [Accepted: 12/21/2023] [Indexed: 02/21/2024]
24
Mao Y, Harvey WT, Porubsky D, Munson KM, Hoekzema K, Lewis AP, Audano PA, Rozanski A, Yang X, Zhang S, Yoo D, Gordon DS, Fair T, Wei X, Logsdon GA, Haukness M, Dishuck PC, Jeong H, Del Rosario R, Bauer VL, Fattor WT, Wilkerson GK, Mao Y, Shi Y, Sun Q, Lu Q, Paten B, Bakken TE, Pollen AA, Feng G, Sawyer SL, Warren WC, Carbone L, Eichler EE. Structurally divergent and recurrently mutated regions of primate genomes. Cell 2024;187:1547-1562.e13. [PMID: 38428424 PMCID: PMC10947866 DOI: 10.1016/j.cell.2024.01.052] [Citation(s) in RCA: 27] [Impact Index Per Article: 27.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/28/2023] [Revised: 11/26/2023] [Accepted: 01/31/2024] [Indexed: 03/03/2024]
25
Pascual-Garrido A, Carvalho S, Almeida-Warren K. Primate archaeology 3.0. AMERICAN JOURNAL OF BIOLOGICAL ANTHROPOLOGY 2024;183:e24835. [PMID: 37671610 DOI: 10.1002/ajpa.24835] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/17/2023] [Revised: 07/25/2023] [Accepted: 08/03/2023] [Indexed: 09/07/2023]
26
Marchi N, Kapopoulou A, Excoffier L. Demogenomic inference from spatially and temporally heterogeneous samples. Mol Ecol Resour 2024;24:e13877. [PMID: 37819677 DOI: 10.1111/1755-0998.13877] [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: 09/15/2023] [Accepted: 09/27/2023] [Indexed: 10/13/2023]
27
Langdon QK, Groh JS, Aguillon SM, Powell DL, Gunn T, Payne C, Baczenas JJ, Donny A, Dodge TO, Du K, Schartl M, Ríos-Cárdenas O, Gutierrez-Rodríguez C, Morris M, Schumer M. Genome evolution is surprisingly predictable after initial hybridization. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2023:2023.12.21.572897. [PMID: 38187753 PMCID: PMC10769416 DOI: 10.1101/2023.12.21.572897] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Indexed: 01/09/2024]
28
Makova KD, Pickett BD, Harris RS, Hartley GA, Cechova M, Pal K, Nurk S, Yoo D, Li Q, Hebbar P, McGrath BC, Antonacci F, Aubel M, Biddanda A, Borchers M, Bomberg E, Bouffard GG, Brooks SY, Carbone L, Carrel L, Carroll A, Chang PC, Chin CS, Cook DE, Craig SJ, de Gennaro L, Diekhans M, Dutra A, Garcia GH, Grady PG, Green RE, Haddad D, Hallast P, Harvey WT, Hickey G, Hillis DA, Hoyt SJ, Jeong H, Kamali K, Kosakovsky Pond SL, LaPolice TM, Lee C, Lewis AP, Loh YHE, Masterson P, McCoy RC, Medvedev P, Miga KH, Munson KM, Pak E, Paten B, Pinto BJ, Potapova T, Rhie A, Rocha JL, Ryabov F, Ryder OA, Sacco S, Shafin K, Shepelev VA, Slon V, Solar SJ, Storer JM, Sudmant PH, Sweetalana, Sweeten A, Tassia MG, Thibaud-Nissen F, Ventura M, Wilson MA, Young AC, Zeng H, Zhang X, Szpiech ZA, Huber CD, Gerton JL, Yi SV, Schatz MC, Alexandrov IA, Koren S, O’Neill RJ, Eichler E, Phillippy AM. The Complete Sequence and Comparative Analysis of Ape Sex Chromosomes. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2023:2023.11.30.569198. [PMID: 38077089 PMCID: PMC10705393 DOI: 10.1101/2023.11.30.569198] [Citation(s) in RCA: 5] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Indexed: 12/24/2023]
29
Anwised P, Moorawong R, Samruan W, Somredngan S, Srisutush J, Laowtammathron C, Aksoy I, Parnpai R, Savatier P. An expedition in the jungle of pluripotent stem cells of non-human primates. Stem Cell Reports 2023;18:2016-2037. [PMID: 37863046 PMCID: PMC10679654 DOI: 10.1016/j.stemcr.2023.09.013] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/16/2023] [Revised: 09/20/2023] [Accepted: 09/21/2023] [Indexed: 10/22/2023]  Open
30
Aghebatrafat AA, Lauber C, Merkel K, Fruth B, Langergraber K, Robbins MM, Wittig RM, Leendertz FH, Calvignac-Spencer S. Evolutionary Insight into the Association between New Jersey Polyomavirus and Humans. Viruses 2023;15:2248. [PMID: 38005925 PMCID: PMC10675294 DOI: 10.3390/v15112248] [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: 09/29/2023] [Revised: 11/05/2023] [Accepted: 11/06/2023] [Indexed: 11/26/2023]  Open
31
Brand CM, Kuang S, Gilbertson EN, McArthur E, Pollard KS, Webster TH, Capra JA. Sequence-based machine learning reveals 3D genome differences between bonobos and chimpanzees. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2023:2023.10.26.564272. [PMID: 37961120 PMCID: PMC10634871 DOI: 10.1101/2023.10.26.564272] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/15/2023]
32
Lee J, Chen S, Monfared RV, Derdeyn P, Leong K, Chang T, Beier K, Baldi P, Alachkar A. Reanalysis of primate brain circadian transcriptomics reveals connectivity-related oscillations. iScience 2023;26:107810. [PMID: 37752952 PMCID: PMC10518731 DOI: 10.1016/j.isci.2023.107810] [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: 05/08/2023] [Revised: 07/22/2023] [Accepted: 08/30/2023] [Indexed: 09/28/2023]  Open
33
Pollen AA, Kilik U, Lowe CB, Camp JG. Human-specific genetics: new tools to explore the molecular and cellular basis of human evolution. Nat Rev Genet 2023;24:687-711. [PMID: 36737647 PMCID: PMC9897628 DOI: 10.1038/s41576-022-00568-4] [Citation(s) in RCA: 48] [Impact Index Per Article: 24.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 12/08/2022] [Indexed: 02/05/2023]
34
Cheng J, Novati G, Pan J, Bycroft C, Žemgulytė A, Applebaum T, Pritzel A, Wong LH, Zielinski M, Sargeant T, Schneider RG, Senior AW, Jumper J, Hassabis D, Kohli P, Avsec Ž. Accurate proteome-wide missense variant effect prediction with AlphaMissense. Science 2023;381:eadg7492. [PMID: 37733863 DOI: 10.1126/science.adg7492] [Citation(s) in RCA: 687] [Impact Index Per Article: 343.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/19/2023] [Accepted: 08/23/2023] [Indexed: 09/23/2023]
35
Yee SW, Ferrández-Peral L, Alentorn P, Fontsere C, Ceylan M, Koleske ML, Handin N, Artegoitia VM, Lara G, Chien HC, Zhou X, Dainat J, Zalevsky A, Sali A, Brand CM, Capra JA, Artursson P, Newman JW, Marques-Bonet T, Giacomini KM. Illuminating the Function of the Orphan Transporter, SLC22A10 in Humans and Other Primates. RESEARCH SQUARE 2023:rs.3.rs-3263845. [PMID: 37790518 PMCID: PMC10543398 DOI: 10.21203/rs.3.rs-3263845/v1] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 10/05/2023]
36
Gautney JR. A new approach to exploratory data analysis in hominin phylogenetic reconstruction. J Hum Evol 2023;182:103412. [PMID: 37499423 DOI: 10.1016/j.jhevol.2023.103412] [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: 09/23/2022] [Revised: 06/30/2023] [Accepted: 07/01/2023] [Indexed: 07/29/2023]
37
Pawar H, Rymbekova A, Cuadros-Espinoza S, Huang X, de Manuel M, van der Valk T, Lobon I, Alvarez-Estape M, Haber M, Dolgova O, Han S, Esteller-Cucala P, Juan D, Ayub Q, Bautista R, Kelley JL, Cornejo OE, Lao O, Andrés AM, Guschanski K, Ssebide B, Cranfield M, Tyler-Smith C, Xue Y, Prado-Martinez J, Marques-Bonet T, Kuhlwilm M. Ghost admixture in eastern gorillas. Nat Ecol Evol 2023;7:1503-1514. [PMID: 37500909 PMCID: PMC10482688 DOI: 10.1038/s41559-023-02145-2] [Citation(s) in RCA: 5] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/19/2022] [Accepted: 06/30/2023] [Indexed: 07/29/2023]
38
Yee SW, Ferrández-Peral L, Alentorn P, Fontsere C, Ceylan M, Koleske ML, Handin N, Artegoitia VM, Lara G, Chien HC, Zhou X, Dainat J, Zalevsky A, Sali A, Brand CM, Capra JA, Artursson P, Newman JW, Marques-Bonet T, Giacomini KM. Illuminating the Function of the Orphan Transporter, SLC22A10 in Humans and Other Primates. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2023:2023.08.08.552553. [PMID: 37609337 PMCID: PMC10441401 DOI: 10.1101/2023.08.08.552553] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 08/24/2023]
39
Chevy ET, Huerta-Sánchez E, Ramachandran S. Integrating sex-bias into studies of archaic introgression on chromosome X. PLoS Genet 2023;19:e1010399. [PMID: 37578977 PMCID: PMC10449224 DOI: 10.1371/journal.pgen.1010399] [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: 08/29/2022] [Revised: 08/24/2023] [Accepted: 07/10/2023] [Indexed: 08/16/2023]  Open
40
Harper CM, Roach CS, Goldstein DM, Sylvester AD. Morphological variation of the Pan talus relative to that of Gorilla. AMERICAN JOURNAL OF BIOLOGICAL ANTHROPOLOGY 2023. [PMID: 37300336 DOI: 10.1002/ajpa.24796] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/02/2022] [Revised: 03/27/2023] [Accepted: 05/27/2023] [Indexed: 06/12/2023]
41
Wu H, Wang Z, Zhang Y, Frantz L, Roos C, Irwin DM, Zhang C, Liu X, Wu D, Huang S, Gu T, Liu J, Yu L. Hybrid origin of a primate, the gray snub-nosed monkey. Science 2023;380:eabl4997. [PMID: 37262139 DOI: 10.1126/science.abl4997] [Citation(s) in RCA: 12] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/17/2021] [Accepted: 07/06/2022] [Indexed: 06/03/2023]
42
Sørensen EF, Harris RA, Zhang L, Raveendran M, Kuderna LFK, Walker JA, Storer JM, Kuhlwilm M, Fontsere C, Seshadri L, Bergey CM, Burrell AS, Bergman J, Phillips-Conroy JE, Shiferaw F, Chiou KL, Chuma IS, Keyyu JD, Fischer J, Gingras MC, Salvi S, Doddapaneni H, Schierup MH, Batzer MA, Jolly CJ, Knauf S, Zinner D, Farh KKH, Marques-Bonet T, Munch K, Roos C, Rogers J. Genome-wide coancestry reveals details of ancient and recent male-driven reticulation in baboons. Science 2023;380:eabn8153. [PMID: 37262153 DOI: 10.1126/science.abn8153] [Citation(s) in RCA: 20] [Impact Index Per Article: 10.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/23/2021] [Accepted: 09/27/2022] [Indexed: 06/03/2023]
43
Kuderna LFK, Gao H, Janiak MC, Kuhlwilm M, Orkin JD, Bataillon T, Manu S, Valenzuela A, Bergman J, Rousselle M, Silva FE, Agueda L, Blanc J, Gut M, de Vries D, Goodhead I, Harris RA, Raveendran M, Jensen A, Chuma IS, Horvath JE, Hvilsom C, Juan D, Frandsen P, Schraiber JG, de Melo FR, Bertuol F, Byrne H, Sampaio I, Farias I, Valsecchi J, Messias M, da Silva MNF, Trivedi M, Rossi R, Hrbek T, Andriaholinirina N, Rabarivola CJ, Zaramody A, Jolly CJ, Phillips-Conroy J, Wilkerson G, Abee C, Simmons JH, Fernandez-Duque E, Kanthaswamy S, Shiferaw F, Wu D, Zhou L, Shao Y, Zhang G, Keyyu JD, Knauf S, Le MD, Lizano E, Merker S, Navarro A, Nadler T, Khor CC, Lee J, Tan P, Lim WK, Kitchener AC, Zinner D, Gut I, Melin AD, Guschanski K, Schierup MH, Beck RMD, Umapathy G, Roos C, Boubli JP, Rogers J, Farh KKH, Bonet TM. A global catalog of whole-genome diversity from 233 primate species. Science 2023;380:906-913. [PMID: 37262161 PMCID: PMC12120848 DOI: 10.1126/science.abn7829] [Citation(s) in RCA: 73] [Impact Index Per Article: 36.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/19/2021] [Accepted: 02/06/2023] [Indexed: 06/03/2023]
44
Gao H, Hamp T, Ede J, Schraiber JG, McRae J, Singer-Berk M, Yang Y, Dietrich ASD, Fiziev PP, Kuderna LFK, Sundaram L, Wu Y, Adhikari A, Field Y, Chen C, Batzoglou S, Aguet F, Lemire G, Reimers R, Balick D, Janiak MC, Kuhlwilm M, Orkin JD, Manu S, Valenzuela A, Bergman J, Rousselle M, Silva FE, Agueda L, Blanc J, Gut M, de Vries D, Goodhead I, Harris RA, Raveendran M, Jensen A, Chuma IS, Horvath JE, Hvilsom C, Juan D, Frandsen P, de Melo FR, Bertuol F, Byrne H, Sampaio I, Farias I, do Amaral JV, Messias M, da Silva MNF, Trivedi M, Rossi R, Hrbek T, Andriaholinirina N, Rabarivola CJ, Zaramody A, Jolly CJ, Phillips-Conroy J, Wilkerson G, Abee C, Simmons JH, Fernandez-Duque E, Kanthaswamy S, Shiferaw F, Wu D, Zhou L, Shao Y, Zhang G, Keyyu JD, Knauf S, Le MD, Lizano E, Merker S, Navarro A, Bataillon T, Nadler T, Khor CC, Lee J, Tan P, Lim WK, Kitchener AC, Zinner D, Gut I, Melin A, Guschanski K, Schierup MH, Beck RMD, Umapathy G, Roos C, Boubli JP, Lek M, Sunyaev S, O'Donnell-Luria A, Rehm HL, Xu J, Rogers J, Marques-Bonet T, Farh KKH. The landscape of tolerated genetic variation in humans and primates. Science 2023;380:eabn8153. [PMID: 37262156 DOI: 10.1126/science.abn8197] [Citation(s) in RCA: 78] [Impact Index Per Article: 39.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/31/2021] [Accepted: 03/22/2023] [Indexed: 06/03/2023]
45
Sørensen EF, Harris RA, Zhang L, Raveendran M, Kuderna LFK, Walker JA, Storer JM, Kuhlwilm M, Fontsere C, Seshadri L, Bergey CM, Burrell AS, Bergmann J, Phillips-Conroy JE, Shiferaw F, Chiou KL, Chuma IS, Keyyu JD, Fischer J, Gingras MC, Salvi S, Doddapaneni H, Schierup MH, Batzer MA, Jolly CJ, Knauf S, Zinner D, Farh KKH, Marques-Bonet T, Munch K, Roos C, Rogers J. Genome-wide coancestry reveals details of ancient and recent male-driven reticulation in baboons. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2023:2023.05.02.539112. [PMID: 37205419 PMCID: PMC10187195 DOI: 10.1101/2023.05.02.539112] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/21/2023]
46
Gao H, Hamp T, Ede J, Schraiber JG, McRae J, Singer-Berk M, Yang Y, Dietrich A, Fiziev P, Kuderna L, Sundaram L, Wu Y, Adhikari A, Field Y, Chen C, Batzoglou S, Aguet F, Lemire G, Reimers R, Balick D, Janiak MC, Kuhlwilm M, Orkin JD, Manu S, Valenzuela A, Bergman J, Rouselle M, Silva FE, Agueda L, Blanc J, Gut M, de Vries D, Goodhead I, Harris RA, Raveendran M, Jensen A, Chuma IS, Horvath J, Hvilsom C, Juan D, Frandsen P, de Melo FR, Bertuol F, Byrne H, Sampaio I, Farias I, do Amaral JV, Messias M, da Silva MNF, Trivedi M, Rossi R, Hrbek T, Andriaholinirina N, Rabarivola CJ, Zaramody A, Jolly CJ, Phillips-Conroy J, Wilkerson G, Abee C, Simmons JH, Fernandez-Duque E, Kanthaswamy S, Shiferaw F, Wu D, Zhou L, Shao Y, Zhang G, Keyyu JD, Knauf S, Le MD, Lizano E, Merker S, Navarro A, Batallion T, Nadler T, Khor CC, Lee J, Tan P, Lim WK, Kitchener AC, Zinner D, Gut I, Melin A, Guschanski K, Schierup MH, Beck RMD, Umapathy G, Roos C, Boubli JP, Lek M, Sunyaev S, O’Donnell A, Rehm H, Xu J, Rogers J, Marques-Bonet T, Kai-How Farh K. The landscape of tolerated genetic variation in humans and primates. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2023:2023.05.01.538953. [PMID: 37205491 PMCID: PMC10187174 DOI: 10.1101/2023.05.01.538953] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/21/2023]
47
Mao Y, Harvey WT, Porubsky D, Munson KM, Hoekzema K, Lewis AP, Audano PA, Rozanski A, Yang X, Zhang S, Gordon DS, Wei X, Logsdon GA, Haukness M, Dishuck PC, Jeong H, Del Rosario R, Bauer VL, Fattor WT, Wilkerson GK, Lu Q, Paten B, Feng G, Sawyer SL, Warren WC, Carbone L, Eichler EE. Structurally divergent and recurrently mutated regions of primate genomes. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2023:2023.03.07.531415. [PMID: 36945442 PMCID: PMC10028934 DOI: 10.1101/2023.03.07.531415] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 03/10/2023]
48
Current advances in primate genomics: novel approaches for understanding evolution and disease. Nat Rev Genet 2023;24:314-331. [PMID: 36599936 DOI: 10.1038/s41576-022-00554-w] [Citation(s) in RCA: 23] [Impact Index Per Article: 11.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 11/07/2022] [Indexed: 01/05/2023]
49
Sarringhaus L, Lewton KL, Iqbal S, Carlson KJ. Ape femoral-humeral rigidities and arboreal locomotion. AMERICAN JOURNAL OF BIOLOGICAL ANTHROPOLOGY 2022;179:624-639. [PMID: 36790629 PMCID: PMC9828227 DOI: 10.1002/ajpa.24632] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 12/19/2021] [Revised: 06/29/2022] [Accepted: 09/13/2022] [Indexed: 11/07/2022]
50
Noguerales V, Ortego J. Genomic evidence of speciation by fusion in a recent radiation of grasshoppers. Evolution 2022;76:2618-2633. [PMID: 35695020 PMCID: PMC9796961 DOI: 10.1111/evo.14508] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/29/2021] [Revised: 03/22/2022] [Accepted: 04/02/2022] [Indexed: 01/22/2023]
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