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For: Zhang D, Rheindt FE, She H, Cheng Y, Song G, Jia C, Qu Y, Alström P, Lei F. Most Genomic Loci Misrepresent the Phylogeny of an Avian Radiation Because of Ancient Gene Flow. Syst Biol 2021;70:961-975. [PMID: 33787929 PMCID: PMC8357342 DOI: 10.1093/sysbio/syab024] [Citation(s) in RCA: 25] [Impact Index Per Article: 8.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/25/2020] [Revised: 03/24/2021] [Accepted: 03/29/2021] [Indexed: 12/11/2022]  Open
Number Cited by Other Article(s)
1
Wang S, Wu L, Zhu Q, Wu J, Tang S, Zhao Y, Cheng Y, Zhang D, Qiao G, Zhang R, Lei F. Trait Variation and Spatiotemporal Dynamics across Avian Secondary Contact Zones. BIOLOGY 2024;13:643. [PMID: 39194581 DOI: 10.3390/biology13080643] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/18/2024] [Revised: 08/16/2024] [Accepted: 08/20/2024] [Indexed: 08/29/2024]
2
Ma XG, Ren YB, Sun H. Introgression and incomplete lineage sorting blurred phylogenetic relationships across the genomes of sclerophyllous oaks from southwest China. Cladistics 2024;40:357-373. [PMID: 38197450 DOI: 10.1111/cla.12570] [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: 11/27/2023] [Accepted: 12/09/2023] [Indexed: 01/11/2024]  Open
3
Zhang D, She H, Wang S, Wang H, Li S, Cheng Y, Song G, Jia C, Qu Y, Rheindt FE, Olsson U, Alström P, Lei F. Phylogenetic Conflict Between Species Tree and Maternally Inherited Gene Trees in a Clade of Emberiza Buntings (Aves: Emberizidae). Syst Biol 2024;73:279-289. [PMID: 38157277 DOI: 10.1093/sysbio/syad078] [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: 07/04/2022] [Revised: 12/06/2023] [Accepted: 12/27/2023] [Indexed: 01/03/2024]  Open
4
Zhang Z, Liu G, Li M. Incomplete lineage sorting and gene flow within Allium (Amayllidaceae). Mol Phylogenet Evol 2024;195:108054. [PMID: 38471599 DOI: 10.1016/j.ympev.2024.108054] [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: 11/30/2023] [Revised: 02/01/2024] [Accepted: 03/07/2024] [Indexed: 03/14/2024]
5
Rancilhac L, Enbody ED, Harris R, Saitoh T, Irestedt M, Liu Y, Lei F, Andersson L, Alström P. Introgression Underlies Phylogenetic Uncertainty But Not Parallel Plumage Evolution in a Recent Songbird Radiation. Syst Biol 2024;73:12-25. [PMID: 37801684 PMCID: PMC11129591 DOI: 10.1093/sysbio/syad062] [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: 04/26/2023] [Revised: 09/11/2023] [Accepted: 10/05/2023] [Indexed: 10/08/2023]  Open
6
Jiang Z, Zang W, Ericson PGP, Song G, Wu S, Feng S, Drovetski SV, Liu G, Zhang D, Saitoh T, Alström P, Edwards SV, Lei F, Qu Y. Gene flow and an anomaly zone complicate phylogenomic inference in a rapidly radiated avian family (Prunellidae). BMC Biol 2024;22:49. [PMID: 38413944 PMCID: PMC10900574 DOI: 10.1186/s12915-024-01848-7] [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: 11/11/2023] [Accepted: 02/15/2024] [Indexed: 02/29/2024]  Open
7
Gao K, He Z, Xiong J, Chen Q, Lai B, Liu F, Chen P, Chen M, Luo W, Huang J, Ding W, Wang H, Pu Y, Zheng L, Jiao Y, Zhang M, Tang Z, Yue Q, Yang D, Yan T. Population structure and adaptability analysis of Schizothorax o'connori based on whole-genome resequencing. BMC Genomics 2024;25:145. [PMID: 38321406 PMCID: PMC10845765 DOI: 10.1186/s12864-024-09975-9] [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: 07/16/2023] [Accepted: 01/04/2024] [Indexed: 02/08/2024]  Open
8
Steenwyk JL, Li Y, Zhou X, Shen XX, Rokas A. Incongruence in the phylogenomics era. Nat Rev Genet 2023;24:834-850. [PMID: 37369847 DOI: 10.1038/s41576-023-00620-x] [Citation(s) in RCA: 9] [Impact Index Per Article: 9.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 05/19/2023] [Indexed: 06/29/2023]
9
Overson RP, Johnson MG, Bechen LL, Kinosian SP, Douglas NA, Fant JB, Hoch PC, Levin RA, Moore MJ, Raguso RA, Wagner WL, Skogen KA, Wickett NJ. A phylogeny of the evening primrose family (Onagraceae) using a target enrichment approach with 303 nuclear loci. BMC Ecol Evol 2023;23:66. [PMID: 37974080 PMCID: PMC10655384 DOI: 10.1186/s12862-023-02151-9] [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: 03/11/2022] [Accepted: 08/16/2023] [Indexed: 11/19/2023]  Open
10
San Jose M, Doorenweerd C, Geib S, Barr N, Dupuis JR, Leblanc L, Kauwe A, Morris KY, Rubinoff D. Interspecific gene flow obscures phylogenetic relationships in an important insect pest species complex. Mol Phylogenet Evol 2023;188:107892. [PMID: 37524217 DOI: 10.1016/j.ympev.2023.107892] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/02/2023] [Revised: 07/07/2023] [Accepted: 07/28/2023] [Indexed: 08/02/2023]
11
Yang C, Dong X, Wang Q, Hou X, Yuan H, Li X. Mitochondrial genome characteristics of six Phylloscopus species and their phylogenetic implication. PeerJ 2023;11:e16233. [PMID: 37842035 PMCID: PMC10576491 DOI: 10.7717/peerj.16233] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/15/2023] [Accepted: 09/14/2023] [Indexed: 10/17/2023]  Open
12
Zhang BL, Chen W, Wang Z, Pang W, Luo MT, Wang S, Shao Y, He WQ, Deng Y, Zhou L, Chen J, Yang MM, Wu Y, Wang L, Fernández-Bellon H, Molloy S, Meunier H, Wanert F, Kuderna L, Marques-Bonet T, Roos C, Qi XG, Li M, Liu Z, Schierup MH, Cooper DN, Liu J, Zheng YT, Zhang G, Wu DD. Comparative genomics reveals the hybrid origin of a macaque group. SCIENCE ADVANCES 2023;9:eadd3580. [PMID: 37262187 PMCID: PMC10413639 DOI: 10.1126/sciadv.add3580] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/06/2022] [Accepted: 01/25/2023] [Indexed: 06/03/2023]
13
Zhou W, Furey NM, Soisook P, Thong VD, Lim BK, Rossiter SJ, Mao X. Diversification and introgression in four chromosomal taxa of the Pearson's horseshoe bat (Rhinolophus pearsoni) group. Mol Phylogenet Evol 2023;183:107784. [PMID: 37040825 DOI: 10.1016/j.ympev.2023.107784] [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: 12/09/2022] [Revised: 03/11/2023] [Accepted: 04/07/2023] [Indexed: 04/13/2023]
14
Feng C, Wang K, Xu W, Yang L, Wanghe K, Sun N, Wu B, Wu F, Yang L, Qiu Q, Gan X, Chen Y, He S. Monsoon boosted radiation of the endemic East Asian carps. SCIENCE CHINA. LIFE SCIENCES 2023;66:563-578. [PMID: 36166180 DOI: 10.1007/s11427-022-2141-1] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/01/2022] [Accepted: 04/21/2022] [Indexed: 10/14/2022]
15
Ottenburghs J, Honka J, Heikkinen ME, Madsen J, Müskens GJDM, Ellegren H. Highly differentiated loci resolve phylogenetic relationships in the Bean Goose complex. BMC Ecol Evol 2023;23:2. [PMID: 36658479 PMCID: PMC9854053 DOI: 10.1186/s12862-023-02103-3] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/26/2022] [Accepted: 01/11/2023] [Indexed: 01/20/2023]  Open
16
Stubbs RL, Theodoridis S, Mora‐Carrera E, Keller B, Yousefi N, Potente G, Léveillé‐Bourret É, Celep F, Kochjarová J, Tedoradze G, Eaton DAR, Conti E. Whole-genome analyses disentangle reticulate evolution of primroses in a biodiversity hotspot. THE NEW PHYTOLOGIST 2023;237:656-671. [PMID: 36210520 PMCID: PMC10099377 DOI: 10.1111/nph.18525] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 07/06/2022] [Accepted: 09/26/2022] [Indexed: 06/16/2023]
17
Wang T, Li TZ, Chen SS, Yang T, Shu JP, Mu YN, Wang KL, Chen JB, Xiang JY, Yan YH. Untying the Gordian knot of plastid phylogenomic conflict: A case from ferns. FRONTIERS IN PLANT SCIENCE 2022;13:918155. [PMID: 36507421 PMCID: PMC9730426 DOI: 10.3389/fpls.2022.918155] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 04/12/2022] [Accepted: 10/11/2022] [Indexed: 06/17/2023]
18
Pang XX, Zhang DY. Impact of Ghost Introgression on Coalescent-based Species Tree Inference and Estimation of Divergence Time. Syst Biol 2022;72:35-49. [PMID: 35799362 DOI: 10.1093/sysbio/syac047] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/17/2022] [Revised: 06/25/2022] [Accepted: 07/05/2022] [Indexed: 11/15/2022]  Open
19
Interpreting phylogenetic conflict: Hybridization in the most speciose genus of lichen-forming fungi. Mol Phylogenet Evol 2022;174:107543. [PMID: 35690378 DOI: 10.1016/j.ympev.2022.107543] [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: 06/11/2021] [Revised: 02/06/2022] [Accepted: 05/13/2022] [Indexed: 11/24/2022]
20
Piller KR, Parker E, Lemmon AR, Moriarty Lemmon E. Investigating the utility of Anchored Hybrid Enrichment data to investigate the relationships among the Killifishes (Actinopterygii: Cyprinodontiformes), a globally distributed group of fishes. Mol Phylogenet Evol 2022;173:107482. [PMID: 35452841 DOI: 10.1016/j.ympev.2022.107482] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/23/2021] [Revised: 04/06/2022] [Accepted: 04/06/2022] [Indexed: 10/18/2022]
21
Ottenburghs J. Avian introgression patterns are consistent with Haldane's Rule. J Hered 2022;113:363-370. [PMID: 35134952 PMCID: PMC9308041 DOI: 10.1093/jhered/esac005] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/19/2021] [Accepted: 01/27/2022] [Indexed: 11/13/2022]  Open
22
Sunde J, Yıldırım Y, Tibblin P, Bekkevold D, Skov C, Nordahl O, Larsson P, Forsman A. Drivers of neutral and adaptive differentiation in pike (Esox lucius) populations from contrasting environments. Mol Ecol 2021;31:1093-1110. [PMID: 34874594 DOI: 10.1111/mec.16315] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/28/2020] [Revised: 11/29/2021] [Accepted: 12/01/2021] [Indexed: 01/28/2023]
23
Hamilton CA, Winiger N, Rubin JJ, Breinholt J, Rougerie R, Kitching IJ, Barber JR, Kawahara AY. Hidden phylogenomic signal helps elucidate arsenurine silkmoth phylogeny and the evolution of body size and wing shape trade-offs. Syst Biol 2021;71:859-874. [PMID: 34791485 DOI: 10.1093/sysbio/syab090] [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] [Received: 05/12/2020] [Revised: 10/29/2021] [Accepted: 11/01/2021] [Indexed: 11/13/2022]  Open
24
Sun Q, Yang Y, Hao X, Xiao J, Liu J, Yuan X. Comparative Mitogenomic Analysis of Five Awl Skippers (Lepidoptera: Hesperiidae: Coeliadinae) and Their Phylogenetic Implications. INSECTS 2021;12:insects12080757. [PMID: 34442323 PMCID: PMC8397065 DOI: 10.3390/insects12080757] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 07/07/2021] [Revised: 08/11/2021] [Accepted: 08/21/2021] [Indexed: 11/16/2022]
25
Suvorov A, Scornavacca C, Fujimoto MS, Bodily P, Clement M, Crandall KA, Whiting MF, Schrider DR, Bybee SM. Deep ancestral introgression shapes evolutionary history of dragonflies and damselflies. Syst Biol 2021;71:526-546. [PMID: 34324671 PMCID: PMC9017697 DOI: 10.1093/sysbio/syab063] [Citation(s) in RCA: 12] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/21/2021] [Revised: 07/20/2021] [Accepted: 07/26/2021] [Indexed: 11/13/2022]  Open
26
Jennings WB. Evolutionary relationships among the snakelike pygopodid lizards: a review of phylogenetic studies of an enigmatic Australian adaptive radiation. PeerJ 2021;9:e11502. [PMID: 34249485 PMCID: PMC8253114 DOI: 10.7717/peerj.11502] [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: 01/09/2021] [Accepted: 05/03/2021] [Indexed: 12/03/2022]  Open
27
Hao X, Liu J, Chiba H, Xiao J, Yuan X. Complete mitochondrial genomes of three skippers in the tribe Aeromachini (Lepidoptera: Hesperiidae: Hesperiinae) and their phylogenetic implications. Ecol Evol 2021;11:8381-8393. [PMID: 34188893 PMCID: PMC8216930 DOI: 10.1002/ece3.7666] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/10/2020] [Revised: 04/19/2021] [Accepted: 04/28/2021] [Indexed: 11/09/2022]  Open
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