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For: Rogers RL, Cridland JM, Shao L, Hu TT, Andolfatto P, Thornton KR. Landscape of standing variation for tandem duplications in Drosophila yakuba and Drosophila simulans. Mol Biol Evol 2014;31:1750-66. [PMID: 24710518 PMCID: PMC4069613 DOI: 10.1093/molbev/msu124] [Citation(s) in RCA: 65] [Impact Index Per Article: 6.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/13/2022]  Open
Number Cited by Other Article(s)
1
Ferreira EA, Moore CC, Ogereau D, Suwalski A, Prigent SR, Rogers RL, Yassin A. Genomic Islands of Divergence Between Drosophila yakuba Subspecies are Predominantly Driven by Chromosomal Inversions and the Recombination Landscape. Mol Ecol 2024:e17627. [PMID: 39690859 DOI: 10.1111/mec.17627] [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: 08/06/2024] [Revised: 11/22/2024] [Accepted: 11/26/2024] [Indexed: 12/19/2024]
2
Brand CL, Oliver GT, Farkas IZ, Buszczak M, Levine MT. Recurrent Duplication and Diversification of a Vital DNA Repair Gene Family Across Drosophila. Mol Biol Evol 2024;41:msae113. [PMID: 38865490 PMCID: PMC11210505 DOI: 10.1093/molbev/msae113] [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: 11/07/2023] [Revised: 05/30/2024] [Accepted: 06/04/2024] [Indexed: 06/14/2024]  Open
3
Ray DD, Flagel L, Schrider DR. IntroUNET: Identifying introgressed alleles via semantic segmentation. PLoS Genet 2024;20:e1010657. [PMID: 38377104 PMCID: PMC10906877 DOI: 10.1371/journal.pgen.1010657] [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: 02/06/2023] [Revised: 03/01/2024] [Accepted: 01/29/2024] [Indexed: 02/22/2024]  Open
4
Ray DD, Flagel L, Schrider DR. IntroUNET: identifying introgressed alleles via semantic segmentation. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2024:2023.02.07.527435. [PMID: 36865105 PMCID: PMC9979274 DOI: 10.1101/2023.02.07.527435] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Indexed: 06/18/2023]
5
Yıldırım B, Vogl C. Purifying selection against spurious splicing signals contributes to the base composition evolution of the polypyrimidine tract. J Evol Biol 2023;36:1295-1312. [PMID: 37564008 PMCID: PMC10946897 DOI: 10.1111/jeb.14205] [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: 03/28/2023] [Revised: 05/31/2023] [Accepted: 06/15/2023] [Indexed: 08/12/2023]
6
Signor S, Vedanayagam J, Kim BY, Wierzbicki F, Kofler R, Lai EC. Rapid evolutionary diversification of the flamenco locus across simulans clade Drosophila species. PLoS Genet 2023;19:e1010914. [PMID: 37643184 PMCID: PMC10495008 DOI: 10.1371/journal.pgen.1010914] [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: 03/07/2023] [Revised: 09/11/2023] [Accepted: 08/09/2023] [Indexed: 08/31/2023]  Open
7
Vedanayagam J, Herbette M, Mudgett H, Lin CJ, Lai CM, McDonough-Goldstein C, Dorus S, Loppin B, Meiklejohn C, Dubruille R, Lai EC. Essential and recurrent roles for hairpin RNAs in silencing de novo sex chromosome conflict in Drosophila simulans. PLoS Biol 2023;21:e3002136. [PMID: 37289846 PMCID: PMC10292708 DOI: 10.1371/journal.pbio.3002136] [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: 11/01/2022] [Revised: 06/26/2023] [Accepted: 04/21/2023] [Indexed: 06/10/2023]  Open
8
Zhou YY, Jin Y, Liu SQ, Xu SL, Huang YX, Xu YS, Shi LG, Wang HB. Genome-wide identification and comparative analysis of lipocalin families in Lepidoptera with an emphasis on Bombyx mori. INSECT SCIENCE 2023;30:15-30. [PMID: 35343650 DOI: 10.1111/1744-7917.13039] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/12/2022] [Revised: 03/10/2022] [Accepted: 03/10/2022] [Indexed: 06/14/2023]
9
Copy Number Variation of the SOX6 Gene and Its Associations with Growth Traits in Ashidan Yak. Animals (Basel) 2022;12:ani12223074. [PMID: 36428302 PMCID: PMC9686495 DOI: 10.3390/ani12223074] [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: 10/24/2022] [Revised: 11/04/2022] [Accepted: 11/07/2022] [Indexed: 11/09/2022]  Open
10
Huang Y, Shukla H, Lee YCG. Species-specific chromatin landscape determines how transposable elements shape genome evolution. eLife 2022;11:81567. [PMID: 35997258 PMCID: PMC9398452 DOI: 10.7554/elife.81567] [Citation(s) in RCA: 5] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/04/2022] [Accepted: 07/15/2022] [Indexed: 11/30/2022]  Open
11
Brand CL, Levine MT. Cross-species incompatibility between a DNA satellite and the Drosophila Spartan homolog poisons germline genome integrity. Curr Biol 2022;32:2962-2971.e4. [PMID: 35643081 PMCID: PMC9283324 DOI: 10.1016/j.cub.2022.05.009] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/05/2022] [Revised: 04/06/2022] [Accepted: 05/05/2022] [Indexed: 12/19/2022]
12
Dosage sensitivity and exon shuffling shape the landscape of polymorphic duplicates in Drosophila and humans. Nat Ecol Evol 2021;6:273-287. [PMID: 34969986 DOI: 10.1038/s41559-021-01614-w] [Citation(s) in RCA: 9] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/04/2021] [Accepted: 11/10/2021] [Indexed: 11/08/2022]
13
Liao BY. Young duplicate genic DNA. Nat Ecol Evol 2021;6:249-250. [PMID: 34969987 DOI: 10.1038/s41559-021-01639-1] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/09/2022]
14
Serrato-Capuchina A, D’Agostino ERR, Peede D, Roy B, Isbell K, Wang J, Matute DR. P-elements strengthen reproductive isolation within the Drosophila simulans species complex. Evolution 2021;75:2425-2440. [PMID: 34463356 PMCID: PMC8772388 DOI: 10.1111/evo.14319] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/31/2020] [Revised: 04/29/2021] [Accepted: 05/06/2021] [Indexed: 11/28/2022]
15
Niu H, Xia P, Hu Y, Zhan C, Li Y, Gong S, Li Y, Ma D. Genome-wide identification of ZF-HD gene family in Triticum aestivum: Molecular evolution mechanism and function analysis. PLoS One 2021;16:e0256579. [PMID: 34559835 PMCID: PMC8462724 DOI: 10.1371/journal.pone.0256579] [Citation(s) in RCA: 10] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/18/2021] [Accepted: 08/11/2021] [Indexed: 12/04/2022]  Open
16
Jackson B, Charlesworth B. Evidence for a force favoring GC over AT at short intronic sites in Drosophila simulans and Drosophila melanogaster. G3 GENES|GENOMES|GENETICS 2021;11:6321237. [PMID: 34544137 PMCID: PMC8496279 DOI: 10.1093/g3journal/jkab240] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 02/13/2021] [Accepted: 07/06/2021] [Indexed: 11/13/2022]
17
McBroome J, Liang D, Corbett-Detig R. Fine-Scale Position Effects Shape the Distribution of Inversion Breakpoints in Drosophila melanogaster. Genome Biol Evol 2021;12:1378-1391. [PMID: 32437518 PMCID: PMC7487137 DOI: 10.1093/gbe/evaa103] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 05/18/2020] [Indexed: 12/20/2022]  Open
18
Genomic analyses of new genes and their phenotypic effects reveal rapid evolution of essential functions in Drosophila development. PLoS Genet 2021;17:e1009654. [PMID: 34242211 PMCID: PMC8270118 DOI: 10.1371/journal.pgen.1009654] [Citation(s) in RCA: 18] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/12/2021] [Accepted: 06/09/2021] [Indexed: 12/27/2022]  Open
19
Vogl C, Mikula LC. A nearly-neutral biallelic Moran model with biased mutation and linear and quadratic selection. Theor Popul Biol 2021;139:1-17. [PMID: 33964284 DOI: 10.1016/j.tpb.2021.03.003] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/18/2020] [Revised: 03/28/2021] [Accepted: 03/29/2021] [Indexed: 01/27/2023]
20
Nandolo W, Mészáros G, Wurzinger M, Banda LJ, Gondwe TN, Mulindwa HA, Nakimbugwe HN, Clark EL, Woodward-Greene MJ, Liu M, Liu GE, Van Tassell CP, Rosen BD, Sölkner J. Detection of copy number variants in African goats using whole genome sequence data. BMC Genomics 2021;22:398. [PMID: 34051743 PMCID: PMC8164248 DOI: 10.1186/s12864-021-07703-1] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/24/2020] [Accepted: 05/11/2021] [Indexed: 12/21/2022]  Open
21
Schwarz F, Wierzbicki F, Senti KA, Kofler R. Tirant Stealthily Invaded Natural Drosophila melanogaster Populations during the Last Century. Mol Biol Evol 2021;38:1482-1497. [PMID: 33247725 PMCID: PMC8042734 DOI: 10.1093/molbev/msaa308] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [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
22
Chakraborty M, Chang CH, Khost DE, Vedanayagam J, Adrion JR, Liao Y, Montooth KL, Meiklejohn CD, Larracuente AM, Emerson JJ. Evolution of genome structure in the Drosophila simulans species complex. Genome Res 2021;31:380-396. [PMID: 33563718 PMCID: PMC7919458 DOI: 10.1101/gr.263442.120] [Citation(s) in RCA: 37] [Impact Index Per Article: 12.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/12/2020] [Accepted: 12/28/2020] [Indexed: 12/25/2022]
23
Rogers RL, Grizzard SL, Titus-McQuillan JE, Bockrath K, Patel S, Wares JP, Garner JT, Moore CC. Gene family amplification facilitates adaptation in freshwater unionid bivalve Megalonaias nervosa. Mol Ecol 2021;30:1155-1173. [PMID: 33382161 DOI: 10.1111/mec.15786] [Citation(s) in RCA: 10] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/31/2020] [Revised: 12/01/2020] [Accepted: 12/14/2020] [Indexed: 01/05/2023]
24
Ferreira EA, Lambert S, Verrier T, Marion-Poll F, Yassin A. Soft Selective Sweep on Chemosensory Genes Correlates with Ancestral Preference for Toxic Noni in a Specialist Drosophila Population. Genes (Basel) 2020;12:genes12010032. [PMID: 33383708 PMCID: PMC7824377 DOI: 10.3390/genes12010032] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/30/2020] [Revised: 12/17/2020] [Accepted: 12/22/2020] [Indexed: 12/14/2022]  Open
25
Saint-Leandre B, Christopher C, Levine MT. Adaptive evolution of an essential telomere protein restricts telomeric retrotransposons. eLife 2020;9:e60987. [PMID: 33350936 PMCID: PMC7755394 DOI: 10.7554/elife.60987] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/13/2020] [Accepted: 11/02/2020] [Indexed: 02/06/2023]  Open
26
Wen Y, He H, Liu H, An Q, Wang D, Ding X, Shi Q, Feng Y, Wang E, Lei C, Zhang Z, Huang Y. Copy number variation of the USP16 gene and its association with milk traits in Chinese Holstein cattle. Anim Biotechnol 2020;33:98-103. [PMID: 32646283 DOI: 10.1080/10495398.2020.1777148] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/24/2022]
27
A Deep Learning Approach for Detecting Copy Number Variation in Next-Generation Sequencing Data. G3-GENES GENOMES GENETICS 2019;9:3575-3582. [PMID: 31455677 PMCID: PMC6829143 DOI: 10.1534/g3.119.400596] [Citation(s) in RCA: 12] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Indexed: 01/13/2023]
28
Structural variants exhibit widespread allelic heterogeneity and shape variation in complex traits. Nat Commun 2019;10:4872. [PMID: 31653862 PMCID: PMC6814777 DOI: 10.1038/s41467-019-12884-1] [Citation(s) in RCA: 84] [Impact Index Per Article: 16.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/27/2018] [Accepted: 09/25/2019] [Indexed: 12/11/2022]  Open
29
Stewart NB, Rogers RL. Chromosomal rearrangements as a source of new gene formation in Drosophila yakuba. PLoS Genet 2019;15:e1008314. [PMID: 31545792 PMCID: PMC6776367 DOI: 10.1371/journal.pgen.1008314] [Citation(s) in RCA: 19] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/31/2019] [Revised: 10/03/2019] [Accepted: 07/17/2019] [Indexed: 11/19/2022]  Open
30
Liu Y, Ramos-Womack M, Han C, Reilly P, Brackett KL, Rogers W, Williams TM, Andolfatto P, Stern DL, Rebeiz M. Changes throughout a Genetic Network Mask the Contribution of Hox Gene Evolution. Curr Biol 2019;29:2157-2166.e6. [PMID: 31257142 DOI: 10.1016/j.cub.2019.05.074] [Citation(s) in RCA: 26] [Impact Index Per Article: 5.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/12/2019] [Revised: 05/10/2019] [Accepted: 05/31/2019] [Indexed: 02/07/2023]
31
Ruzicka F, Hill MS, Pennell TM, Flis I, Ingleby FC, Mott R, Fowler K, Morrow EH, Reuter M. Genome-wide sexually antagonistic variants reveal long-standing constraints on sexual dimorphism in fruit flies. PLoS Biol 2019;17:e3000244. [PMID: 31022179 PMCID: PMC6504117 DOI: 10.1371/journal.pbio.3000244] [Citation(s) in RCA: 64] [Impact Index Per Article: 12.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/01/2019] [Revised: 05/07/2019] [Accepted: 04/09/2019] [Indexed: 01/02/2023]  Open
32
Characterization and evolutionary dynamics of complex regions in eukaryotic genomes. SCIENCE CHINA-LIFE SCIENCES 2019;62:467-488. [PMID: 30810961 DOI: 10.1007/s11427-018-9458-0] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/01/2018] [Accepted: 11/05/2018] [Indexed: 01/07/2023]
33
Li J, Jiang L, Wu CI, Lu X, Fang S, Ting CT. Small Segmental Duplications in Drosophila-High Rate of Emergence and Elimination. Genome Biol Evol 2019;11:486-496. [PMID: 30689862 PMCID: PMC6380325 DOI: 10.1093/gbe/evz011] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 01/19/2019] [Indexed: 12/12/2022]  Open
34
Bonner AM, Hawley RS. Functional Consequences of the Evolution of Matrimony, a Meiosis-Specific Inhibitor of Polo Kinase. Mol Biol Evol 2019;36:69-83. [PMID: 30351378 PMCID: PMC6340472 DOI: 10.1093/molbev/msy197] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/28/2022]  Open
35
Meiklejohn CD, Landeen EL, Gordon KE, Rzatkiewicz T, Kingan SB, Geneva AJ, Vedanayagam JP, Muirhead CA, Garrigan D, Stern DL, Presgraves DC. Gene flow mediates the role of sex chromosome meiotic drive during complex speciation. eLife 2018;7:e35468. [PMID: 30543325 PMCID: PMC6292695 DOI: 10.7554/elife.35468] [Citation(s) in RCA: 44] [Impact Index Per Article: 7.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/28/2018] [Accepted: 11/15/2018] [Indexed: 11/13/2022]  Open
36
Im JH, Lazzaro BP. Population genetic analysis of autophagy and phagocytosis genes in Drosophila melanogaster and D. simulans. PLoS One 2018;13:e0205024. [PMID: 30281656 PMCID: PMC6169979 DOI: 10.1371/journal.pone.0205024] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/20/2018] [Accepted: 09/18/2018] [Indexed: 12/03/2022]  Open
37
Support for the Dominance Theory in Drosophila Transcriptomes. Genetics 2018;210:703-718. [PMID: 30131345 PMCID: PMC6216581 DOI: 10.1534/genetics.118.301229] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/04/2018] [Accepted: 08/10/2018] [Indexed: 12/14/2022]  Open
38
Gaut BS, Seymour DK, Liu Q, Zhou Y. Demography and its effects on genomic variation in crop domestication. NATURE PLANTS 2018;4:512-520. [PMID: 30061748 DOI: 10.1038/s41477-018-0210-1] [Citation(s) in RCA: 122] [Impact Index Per Article: 20.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/11/2018] [Revised: 06/13/2018] [Accepted: 06/27/2018] [Indexed: 05/20/2023]
39
Schrider DR, Ayroles J, Matute DR, Kern AD. Supervised machine learning reveals introgressed loci in the genomes of Drosophila simulans and D. sechellia. PLoS Genet 2018;14:e1007341. [PMID: 29684059 PMCID: PMC5933812 DOI: 10.1371/journal.pgen.1007341] [Citation(s) in RCA: 73] [Impact Index Per Article: 12.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/25/2017] [Revised: 05/03/2018] [Accepted: 03/28/2018] [Indexed: 12/30/2022]  Open
40
VanKuren NW, Long M. Gene duplicates resolving sexual conflict rapidly evolved essential gametogenesis functions. Nat Ecol Evol 2018;2:705-712. [PMID: 29459709 PMCID: PMC5866764 DOI: 10.1038/s41559-018-0471-0] [Citation(s) in RCA: 57] [Impact Index Per Article: 9.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/07/2017] [Accepted: 01/05/2018] [Indexed: 02/04/2023]
41
McGurk MP, Barbash DA. Double insertion of transposable elements provides a substrate for the evolution of satellite DNA. Genome Res 2018;28:714-725. [PMID: 29588362 PMCID: PMC5932611 DOI: 10.1101/gr.231472.117] [Citation(s) in RCA: 46] [Impact Index Per Article: 7.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/20/2017] [Accepted: 03/22/2018] [Indexed: 02/06/2023]
42
Turissini DA, McGirr JA, Patel SS, David JR, Matute DR. The Rate of Evolution of Postmating-Prezygotic Reproductive Isolation in Drosophila. Mol Biol Evol 2018;35:312-334. [PMID: 29048573 PMCID: PMC5850467 DOI: 10.1093/molbev/msx271] [Citation(s) in RCA: 57] [Impact Index Per Article: 9.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/30/2022]  Open
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Chakraborty M, VanKuren NW, Zhao R, Zhang X, Kalsow S, Emerson JJ. Hidden genetic variation shapes the structure of functional elements in Drosophila. Nat Genet 2018;50:20-25. [PMID: 29255259 PMCID: PMC5742068 DOI: 10.1038/s41588-017-0010-y] [Citation(s) in RCA: 94] [Impact Index Per Article: 15.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/15/2017] [Accepted: 11/10/2017] [Indexed: 12/31/2022]
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Levin TC, Malik HS. Rapidly Evolving Toll-3/4 Genes Encode Male-Specific Toll-Like Receptors in Drosophila. Mol Biol Evol 2017;34:2307-2323. [PMID: 28541576 PMCID: PMC5850136 DOI: 10.1093/molbev/msx168] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/30/2022]  Open
45
Jackson BC, Campos JL, Haddrill PR, Charlesworth B, Zeng K. Variation in the Intensity of Selection on Codon Bias over Time Causes Contrasting Patterns of Base Composition Evolution in Drosophila. Genome Biol Evol 2017;9:102-123. [PMID: 28082609 PMCID: PMC5381600 DOI: 10.1093/gbe/evw291] [Citation(s) in RCA: 24] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 12/07/2016] [Indexed: 12/11/2022]  Open
46
Turissini DA, Matute DR. Fine scale mapping of genomic introgressions within the Drosophila yakuba clade. PLoS Genet 2017;13:e1006971. [PMID: 28873409 PMCID: PMC5600410 DOI: 10.1371/journal.pgen.1006971] [Citation(s) in RCA: 56] [Impact Index Per Article: 8.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/13/2017] [Revised: 09/15/2017] [Accepted: 08/09/2017] [Indexed: 12/15/2022]  Open
47
Tandem duplications lead to novel expression patterns through exon shuffling in Drosophila yakuba. PLoS Genet 2017;13:e1006795. [PMID: 28531189 PMCID: PMC5460883 DOI: 10.1371/journal.pgen.1006795] [Citation(s) in RCA: 40] [Impact Index Per Article: 5.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/08/2015] [Revised: 06/06/2017] [Accepted: 05/03/2017] [Indexed: 01/06/2023]  Open
48
Molecular Population Genetics. Genetics 2017;205:1003-1035. [PMID: 28270526 PMCID: PMC5340319 DOI: 10.1534/genetics.116.196493] [Citation(s) in RCA: 55] [Impact Index Per Article: 7.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/03/2016] [Accepted: 11/08/2016] [Indexed: 02/01/2023]  Open
49
Excess of genomic defects in a woolly mammoth on Wrangel island. PLoS Genet 2017;13:e1006601. [PMID: 28253255 PMCID: PMC5333797 DOI: 10.1371/journal.pgen.1006601] [Citation(s) in RCA: 65] [Impact Index Per Article: 9.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/20/2016] [Accepted: 01/24/2017] [Indexed: 01/31/2023]  Open
50
Hu XS, Yeh FC, Hu Y, Deng LT, Ennos RA, Chen X. High mutation rates explain low population genetic divergence at copy-number-variable loci in Homo sapiens. Sci Rep 2017;7:43178. [PMID: 28225073 PMCID: PMC5320550 DOI: 10.1038/srep43178] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/10/2016] [Accepted: 01/19/2017] [Indexed: 11/09/2022]  Open
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