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For: Racimo F. Testing for Ancient Selection Using Cross-population Allele Frequency Differentiation. Genetics 2016;202:733-50. [PMID: 26596347 DOI: 10.1534/genetics.115.178095] [Citation(s) in RCA: 73] [Impact Index Per Article: 8.1] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/11/2015] [Accepted: 11/18/2015] [Indexed: 12/18/2022]  Open
Number Cited by Other Article(s)
1
Wang Y, Duchen P, Chávez A, Sree KS, Appenroth KJ, Zhao H, Höfer M, Huber M, Xu S. Population genomics and epigenomics of Spirodela polyrhiza provide insights into the evolution of facultative asexuality. Commun Biol 2024;7:581. [PMID: 38755313 PMCID: PMC11099151 DOI: 10.1038/s42003-024-06266-7] [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: 08/01/2023] [Accepted: 04/30/2024] [Indexed: 05/18/2024]  Open
2
Peyrégne S, Slon V, Kelso J. More than a decade of genetic research on the Denisovans. Nat Rev Genet 2024;25:83-103. [PMID: 37723347 DOI: 10.1038/s41576-023-00643-4] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 07/19/2023] [Indexed: 09/20/2023]
3
Amin MR, Hasan M, Arnab SP, DeGiorgio M. Tensor Decomposition-based Feature Extraction and Classification to Detect Natural Selection from Genomic Data. Mol Biol Evol 2023;40:msad216. [PMID: 37772983 PMCID: PMC10581699 DOI: 10.1093/molbev/msad216] [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: 03/02/2023] [Revised: 08/10/2023] [Accepted: 09/14/2023] [Indexed: 09/30/2023]  Open
4
Amin MR, Hasan M, Arnab SP, DeGiorgio M. Tensor decomposition based feature extraction and classification to detect natural selection from genomic data. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2023:2023.03.27.527731. [PMID: 37034767 PMCID: PMC10081272 DOI: 10.1101/2023.03.27.527731] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/19/2023]
5
Genomics-informed prebreeding unlocks the diversity in genebanks for wheat improvement. Nat Genet 2022;54:1544-1552. [DOI: 10.1038/s41588-022-01189-7] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/08/2021] [Accepted: 08/18/2022] [Indexed: 11/06/2022]
6
Pawar H, Ostridge HJ, Schmidt JM, Andrés AM. Genetic adaptations to SIV across chimpanzee populations. PLoS Genet 2022;18:e1010337. [PMID: 36007015 PMCID: PMC9467346 DOI: 10.1371/journal.pgen.1010337] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/03/2021] [Revised: 09/12/2022] [Accepted: 07/12/2022] [Indexed: 11/18/2022]  Open
7
Lin X, Zhang N, Song H, Lin K, Pang E. Population-specific, recent positive selection signatures in cultivated Cucumis sativus L. (cucumber). G3 GENES|GENOMES|GENETICS 2022;12:6585339. [PMID: 35554526 PMCID: PMC9258548 DOI: 10.1093/g3journal/jkac119] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 03/17/2022] [Accepted: 05/03/2022] [Indexed: 11/13/2022]
8
Temporal mapping of derived high-frequency gene variants supports the mosaic nature of the evolution of Homo sapiens. Sci Rep 2022;12:9937. [PMID: 35705575 PMCID: PMC9200848 DOI: 10.1038/s41598-022-13589-0] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/12/2022] [Accepted: 05/25/2022] [Indexed: 11/25/2022]  Open
9
Kolesnikov NA, Kharkov VN, Zarubin AA, Voevoda MI, Gubina MA, Shtygasheva OV, Maksimova NR, Sukhomyasova AL, Stepanov VA. Signals of Directed Selection in the Indigenous Populations of Siberia. RUSS J GENET+ 2022. [DOI: 10.1134/s102279542204007x] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/23/2022]
10
Bednarik RG, Saniotis A, Henneberg M. Auto-domestication hypothesis and the rise in mental disorders in modern humans. Med Hypotheses 2022. [DOI: 10.1016/j.mehy.2022.110874] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/18/2022]
11
DeGiorgio M, Szpiech ZA. A spatially aware likelihood test to detect sweeps from haplotype distributions. PLoS Genet 2022;18:e1010134. [PMID: 35404934 PMCID: PMC9022890 DOI: 10.1371/journal.pgen.1010134] [Citation(s) in RCA: 7] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/18/2021] [Revised: 04/21/2022] [Accepted: 03/04/2022] [Indexed: 01/13/2023]  Open
12
Cheng JY, Stern AJ, Racimo F, Nielsen R. Detecting Selection in Multiple Populations by Modeling Ancestral Admixture Components. Mol Biol Evol 2022;39:msab294. [PMID: 34626111 PMCID: PMC8763095 DOI: 10.1093/molbev/msab294] [Citation(s) in RCA: 9] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/26/2022]  Open
13
Levi G, de Lombares C, Giuliani C, Iannuzzi V, Aouci R, Garagnani P, Franceschi C, Grimaud-Hervé D, Narboux-Nême N. DLX5/6 GABAergic Expression Affects Social Vocalization: Implications for Human Evolution. Mol Biol Evol 2021;38:4748-4764. [PMID: 34132815 PMCID: PMC8557472 DOI: 10.1093/molbev/msab181] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/15/2022]  Open
14
Wang Y, Zhao B, Choi J, Lee EA. Genomic approaches to trace the history of human brain evolution with an emerging opportunity for transposon profiling of ancient humans. Mob DNA 2021;12:22. [PMID: 34663455 PMCID: PMC8525043 DOI: 10.1186/s13100-021-00250-2] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/21/2021] [Accepted: 09/27/2021] [Indexed: 12/17/2022]  Open
15
An etiology of human modernity. ANTHROPOLOGICAL REVIEW 2021. [DOI: 10.2478/anre-2021-0020] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022]  Open
16
Benítez-Burraco A, Chekalin E, Bruskin S, Tatarinova T, Morozova I. Recent selection of candidate genes for mammal domestication in Europeans and language change in Europe: a hypothesis. Ann Hum Biol 2021;48:313-320. [PMID: 34241552 DOI: 10.1080/03014460.2021.1936634] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/20/2022]
17
Muthuirulan P, Zhao D, Young M, Richard D, Liu Z, Emami A, Portilla G, Hosseinzadeh S, Cao J, Maridas D, Sedlak M, Menghini D, Cheng L, Li L, Ding X, Ding Y, Rosen V, Kiapour AM, Capellini TD. Joint disease-specificity at the regulatory base-pair level. Nat Commun 2021;12:4161. [PMID: 34230488 PMCID: PMC8260791 DOI: 10.1038/s41467-021-24345-9] [Citation(s) in RCA: 11] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/17/2020] [Accepted: 06/16/2021] [Indexed: 02/06/2023]  Open
18
García-Pérez R, Esteller-Cucala P, Mas G, Lobón I, Di Carlo V, Riera M, Kuhlwilm M, Navarro A, Blancher A, Di Croce L, Gómez-Skarmeta JL, Juan D, Marquès-Bonet T. Epigenomic profiling of primate lymphoblastoid cell lines reveals the evolutionary patterns of epigenetic activities in gene regulatory architectures. Nat Commun 2021;12:3116. [PMID: 34035253 PMCID: PMC8149829 DOI: 10.1038/s41467-021-23397-1] [Citation(s) in RCA: 16] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/23/2020] [Accepted: 04/21/2021] [Indexed: 02/04/2023]  Open
19
Stepanova V, Moczulska KE, Vacano GN, Kurochkin I, Ju X, Riesenberg S, Macak D, Maricic T, Dombrowski L, Schörnig M, Anastassiadis K, Baker O, Naumann R, Khrameeva E, Vanushkina A, Stekolshchikova E, Egorova A, Tkachev A, Mazzarino R, Duval N, Zubkov D, Giavalisco P, Wilkinson TG, Patterson D, Khaitovich P, Pääbo S. Reduced purine biosynthesis in humans after their divergence from Neandertals. eLife 2021;10:58741. [PMID: 33942714 PMCID: PMC8133780 DOI: 10.7554/elife.58741] [Citation(s) in RCA: 9] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/09/2020] [Accepted: 05/02/2021] [Indexed: 12/02/2022]  Open
20
Schlebusch CM, Sjödin P, Breton G, Günther T, Naidoo T, Hollfelder N, Sjöstrand AE, Xu J, Gattepaille LM, Vicente M, Scofield DG, Malmström H, de Jongh M, Lombard M, Soodyall H, Jakobsson M. Khoe-San Genomes Reveal Unique Variation and Confirm the Deepest Population Divergence in Homo sapiens. Mol Biol Evol 2021;37:2944-2954. [PMID: 32697301 PMCID: PMC7530619 DOI: 10.1093/molbev/msaa140] [Citation(s) in RCA: 36] [Impact Index Per Article: 12.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/24/2022]  Open
21
Harris AM, DeGiorgio M. A Likelihood Approach for Uncovering Selective Sweep Signatures from Haplotype Data. Mol Biol Evol 2021;37:3023-3046. [PMID: 32392293 PMCID: PMC7530616 DOI: 10.1093/molbev/msaa115] [Citation(s) in RCA: 16] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/11/2022]  Open
22
O'Rourke T, Martins PT, Asano R, Tachibana RO, Okanoya K, Boeckx C. Capturing the Effects of Domestication on Vocal Learning Complexity. Trends Cogn Sci 2021;25:462-474. [PMID: 33810982 DOI: 10.1016/j.tics.2021.03.007] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/27/2020] [Revised: 03/08/2021] [Accepted: 03/08/2021] [Indexed: 11/28/2022]
23
Lindo J, DeGiorgio M. Understanding the Adaptive Evolutionary Histories of South American Ancient and Present-Day Populations via Genomics. Genes (Basel) 2021;12:360. [PMID: 33801556 PMCID: PMC8001801 DOI: 10.3390/genes12030360] [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: 01/28/2021] [Revised: 02/18/2021] [Accepted: 02/22/2021] [Indexed: 12/03/2022]  Open
24
Dannemann M. The Population-Specific Impact of Neandertal Introgression on Human Disease. Genome Biol Evol 2021;13:6008690. [PMID: 33247712 PMCID: PMC7851588 DOI: 10.1093/gbe/evaa250] [Citation(s) in RCA: 16] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 11/22/2020] [Indexed: 12/20/2022]  Open
25
Werren EA, Garcia O, Bigham AW. Identifying adaptive alleles in the human genome: from selection mapping to functional validation. Hum Genet 2020;140:241-276. [PMID: 32728809 DOI: 10.1007/s00439-020-02206-7] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/19/2020] [Accepted: 07/07/2020] [Indexed: 12/19/2022]
26
Harris AM, DeGiorgio M. Identifying and Classifying Shared Selective Sweeps from Multilocus Data. Genetics 2020;215:143-171. [PMID: 32152048 PMCID: PMC7198270 DOI: 10.1534/genetics.120.303137] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/22/2019] [Accepted: 02/29/2020] [Indexed: 11/18/2022]  Open
27
Richard D, Liu Z, Cao J, Kiapour AM, Willen J, Yarlagadda S, Jagoda E, Kolachalama VB, Sieker JT, Chang GH, Muthuirulan P, Young M, Masson A, Konrad J, Hosseinzadeh S, Maridas DE, Rosen V, Krawetz R, Roach N, Capellini TD. Evolutionary Selection and Constraint on Human Knee Chondrocyte Regulation Impacts Osteoarthritis Risk. Cell 2020;181:362-381.e28. [PMID: 32220312 PMCID: PMC7179902 DOI: 10.1016/j.cell.2020.02.057] [Citation(s) in RCA: 56] [Impact Index Per Article: 14.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/10/2019] [Revised: 12/10/2019] [Accepted: 02/26/2020] [Indexed: 02/06/2023]
28
Naval-Sanchez M, McWilliam S, Evans B, Yáñez JM, Houston RD, Kijas JW. Changed Patterns of Genomic Variation Following Recent Domestication: Selection Sweeps in Farmed Atlantic Salmon. Front Genet 2020;11:264. [PMID: 32318091 PMCID: PMC7147387 DOI: 10.3389/fgene.2020.00264] [Citation(s) in RCA: 12] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/03/2019] [Accepted: 03/05/2020] [Indexed: 12/30/2022]  Open
29
Glutamate receptors in domestication and modern human evolution. Neurosci Biobehav Rev 2020;108:341-357. [DOI: 10.1016/j.neubiorev.2019.10.004] [Citation(s) in RCA: 23] [Impact Index Per Article: 5.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/23/2019] [Revised: 09/28/2019] [Accepted: 10/07/2019] [Indexed: 02/08/2023]
30
Zanella M, Vitriolo A, Andirko A, Martins PT, Sturm S, O’Rourke T, Laugsch M, Malerba N, Skaros A, Trattaro S, Germain PL, Mihailovic M, Merla G, Rada-Iglesias A, Boeckx C, Testa G. Dosage analysis of the 7q11.23 Williams region identifies BAZ1B as a major human gene patterning the modern human face and underlying self-domestication. SCIENCE ADVANCES 2019;5:eaaw7908. [PMID: 31840056 PMCID: PMC6892627 DOI: 10.1126/sciadv.aaw7908] [Citation(s) in RCA: 47] [Impact Index Per Article: 9.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/24/2019] [Accepted: 09/26/2019] [Indexed: 05/10/2023]
31
Satta Y, Zheng W, Nishiyama KV, Iwasaki RL, Hayakawa T, Fujito NT, Takahata N. Two-dimensional site frequency spectrum for detecting, classifying and dating incomplete selective sweeps. Genes Genet Syst 2019;94:283-300. [DOI: 10.1266/ggs.19-00012] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/23/2022]  Open
32
Schmidt JM, de Manuel M, Marques-Bonet T, Castellano S, Andrés AM. The impact of genetic adaptation on chimpanzee subspecies differentiation. PLoS Genet 2019;15:e1008485. [PMID: 31765391 PMCID: PMC6901233 DOI: 10.1371/journal.pgen.1008485] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/10/2019] [Revised: 12/09/2019] [Accepted: 10/17/2019] [Indexed: 12/25/2022]  Open
33
Refoyo-Martínez A, da Fonseca RR, Halldórsdóttir K, Árnason E, Mailund T, Racimo F. Identifying loci under positive selection in complex population histories. Genome Res 2019;29:1506-1520. [PMID: 31362936 PMCID: PMC6724678 DOI: 10.1101/gr.246777.118] [Citation(s) in RCA: 28] [Impact Index Per Article: 5.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/26/2018] [Accepted: 07/23/2019] [Indexed: 12/24/2022]
34
Kim JY, Jeong S, Kim KH, Lim WJ, Lee HY, Kim N. Discovery of Genomic Characteristics and Selection Signatures in Korean Indigenous Goats Through Comparison of 10 Goat Breeds. Front Genet 2019;10:699. [PMID: 31440273 PMCID: PMC6694180 DOI: 10.3389/fgene.2019.00699] [Citation(s) in RCA: 15] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/23/2018] [Accepted: 07/03/2019] [Indexed: 12/16/2022]  Open
35
Lee KM, Coop G. Population genomics perspectives on convergent adaptation. Philos Trans R Soc Lond B Biol Sci 2019;374:20180236. [PMID: 31154979 PMCID: PMC6560269 DOI: 10.1098/rstb.2018.0236] [Citation(s) in RCA: 40] [Impact Index Per Article: 8.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 12/21/2018] [Indexed: 01/12/2023]  Open
36
Fernandes V, Brucato N, Ferreira JC, Pedro N, Cavadas B, Ricaut FX, Alshamali F, Pereira L. Genome-Wide Characterization of Arabian Peninsula Populations: Shedding Light on the History of a Fundamental Bridge between Continents. Mol Biol Evol 2019;36:575-586. [PMID: 30649405 DOI: 10.1093/molbev/msz005] [Citation(s) in RCA: 27] [Impact Index Per Article: 5.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/17/2022]  Open
37
Kuhlwilm M, Boeckx C. A catalog of single nucleotide changes distinguishing modern humans from archaic hominins. Sci Rep 2019;9:8463. [PMID: 31186485 PMCID: PMC6560109 DOI: 10.1038/s41598-019-44877-x] [Citation(s) in RCA: 40] [Impact Index Per Article: 8.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/31/2019] [Accepted: 05/24/2019] [Indexed: 01/06/2023]  Open
38
Librado P, Orlando L. Detecting Signatures of Positive Selection along Defined Branches of a Population Tree Using LSD. Mol Biol Evol 2019;35:1520-1535. [PMID: 29617830 PMCID: PMC5967574 DOI: 10.1093/molbev/msy053] [Citation(s) in RCA: 23] [Impact Index Per Article: 4.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/18/2022]  Open
39
Yang X, Song J, Todd J, Peng Z, Paudel D, Luo Z, Ma X, You Q, Hanson E, Zhao Z, Zhao Y, Zhang J, Ming R, Wang J. Target enrichment sequencing of 307 germplasm accessions identified ancestry of ancient and modern hybrids and signatures of adaptation and selection in sugarcane (Saccharum spp.), a 'sweet' crop with 'bitter' genomes. PLANT BIOTECHNOLOGY JOURNAL 2019;17:488-498. [PMID: 30051590 PMCID: PMC6335080 DOI: 10.1111/pbi.12992] [Citation(s) in RCA: 17] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/10/2018] [Revised: 07/18/2018] [Accepted: 07/21/2018] [Indexed: 05/07/2023]
40
Detection and Classification of Hard and Soft Sweeps from Unphased Genotypes by Multilocus Genotype Identity. Genetics 2018;210:1429-1452. [PMID: 30315068 DOI: 10.1534/genetics.118.301502] [Citation(s) in RCA: 40] [Impact Index Per Article: 6.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/03/2018] [Accepted: 10/08/2018] [Indexed: 11/18/2022]  Open
41
Schlebusch CM, Jakobsson M. Tales of Human Migration, Admixture, and Selection in Africa. Annu Rev Genomics Hum Genet 2018;19:405-428. [DOI: 10.1146/annurev-genom-083117-021759] [Citation(s) in RCA: 55] [Impact Index Per Article: 9.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/09/2022]
42
Guichard E, Peona V, Malagoli Tagliazucchi G, Abitante L, Jagoda E, Musella M, Ricci M, Rubio-Roldán A, Sarno S, Luiselli D, Pettener D, Taccioli C, Pagani L, Garcia-Perez JL, Boattini A. Impact of non-LTR retrotransposons in the differentiation and evolution of anatomically modern humans. Mob DNA 2018;9:28. [PMID: 30147753 PMCID: PMC6094920 DOI: 10.1186/s13100-018-0133-4] [Citation(s) in RCA: 12] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/07/2018] [Accepted: 08/07/2018] [Indexed: 12/31/2022]  Open
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Pendleton AL, Shen F, Taravella AM, Emery S, Veeramah KR, Boyko AR, Kidd JM. Comparison of village dog and wolf genomes highlights the role of the neural crest in dog domestication. BMC Biol 2018;16:64. [PMID: 29950181 PMCID: PMC6022502 DOI: 10.1186/s12915-018-0535-2] [Citation(s) in RCA: 89] [Impact Index Per Article: 14.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/27/2018] [Accepted: 05/23/2018] [Indexed: 02/07/2023]  Open
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Satta Y, Fujito NT, Takahata N. Nonequilibrium Neutral Theory for Hitchhikers. Mol Biol Evol 2018;35:1362-1365. [PMID: 29722819 DOI: 10.1093/molbev/msy093] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/14/2022]  Open
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Weigand H, Leese F. Detecting signatures of positive selection in non-model species using genomic data. Zool J Linn Soc 2018. [DOI: 10.1093/zoolinnean/zly007] [Citation(s) in RCA: 43] [Impact Index Per Article: 7.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/14/2022]
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Racimo F, Berg JJ, Pickrell JK. Detecting Polygenic Adaptation in Admixture Graphs. Genetics 2018;208:1565-1584. [PMID: 29348143 PMCID: PMC5887149 DOI: 10.1534/genetics.117.300489] [Citation(s) in RCA: 73] [Impact Index Per Article: 12.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/08/2017] [Accepted: 01/16/2018] [Indexed: 01/09/2023]  Open
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Jagoda E, Lawson DJ, Wall JD, Lambert D, Muller C, Westaway M, Leavesley M, Capellini TD, Mirazón Lahr M, Gerbault P, Thomas MG, Migliano AB, Willerslev E, Metspalu M, Pagani L. Disentangling Immediate Adaptive Introgression from Selection on Standing Introgressed Variation in Humans. Mol Biol Evol 2018;35:623-630. [PMID: 29220488 PMCID: PMC5850494 DOI: 10.1093/molbev/msx314] [Citation(s) in RCA: 35] [Impact Index Per Article: 5.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/22/2022]  Open
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Yew CW, Lu D, Deng L, Wong LP, Ong RTH, Lu Y, Wang X, Yunus Y, Aghakhanian F, Mokhtar SS, Hoque MZ, Voo CLY, Abdul Rahman T, Bhak J, Phipps ME, Xu S, Teo YY, Kumar SV, Hoh BP. Genomic structure of the native inhabitants of Peninsular Malaysia and North Borneo suggests complex human population history in Southeast Asia. Hum Genet 2018;137:161-173. [DOI: 10.1007/s00439-018-1869-0] [Citation(s) in RCA: 18] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/08/2017] [Accepted: 01/22/2018] [Indexed: 11/28/2022]
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Cheng X, Xu C, DeGiorgio M. Fast and robust detection of ancestral selective sweeps. Mol Ecol 2017;26:6871-6891. [DOI: 10.1111/mec.14416] [Citation(s) in RCA: 21] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/15/2017] [Revised: 10/16/2017] [Accepted: 10/23/2017] [Indexed: 01/01/2023]
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Theofanopoulou C, Gastaldon S, O’Rourke T, Samuels BD, Messner A, Martins PT, Delogu F, Alamri S, Boeckx C. Self-domestication in Homo sapiens: Insights from comparative genomics. PLoS One 2017;12:e0185306. [PMID: 29045412 PMCID: PMC5646786 DOI: 10.1371/journal.pone.0185306] [Citation(s) in RCA: 77] [Impact Index Per Article: 11.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/24/2017] [Accepted: 09/11/2017] [Indexed: 02/07/2023]  Open
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