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For: Simmons MP, Gatesy J. Coalescence vs. concatenation: Sophisticated analyses vs. first principles applied to rooting the angiosperms. Mol Phylogenet Evol 2015;91:98-122. [DOI: 10.1016/j.ympev.2015.05.011] [Citation(s) in RCA: 64] [Impact Index Per Article: 7.1] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/12/2015] [Revised: 05/01/2015] [Accepted: 05/14/2015] [Indexed: 11/24/2022]
Number Cited by Other Article(s)
1
Ané C, Fogg J, Allman ES, Baños H, Rhodes JA. Anomalous networks under the multispecies coalescent: theory and prevalence. J Math Biol 2024;88:29. [PMID: 38372830 DOI: 10.1007/s00285-024-02050-7] [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: 07/15/2023] [Revised: 01/18/2024] [Accepted: 01/21/2024] [Indexed: 02/20/2024]
2
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]
3
Zhang DF, He W, Shao Z, Ahmed I, Zhang Y, Li WJ, Zhao Z. EasyCGTree: a pipeline for prokaryotic phylogenomic analysis based on core gene sets. BMC Bioinformatics 2023;24:390. [PMID: 37838689 PMCID: PMC10576351 DOI: 10.1186/s12859-023-05527-2] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/06/2023] [Accepted: 10/10/2023] [Indexed: 10/16/2023]  Open
4
Simmons MP, Goloboff PA, Stöver BC, Springer MS, Gatesy J. Quantification of congruence among gene trees with polytomies using overall success of resolution for phylogenomic coalescent analyses. Cladistics 2023;39:418-436. [PMID: 37096985 DOI: 10.1111/cla.12540] [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: 12/27/2022] [Revised: 02/22/2023] [Accepted: 03/24/2023] [Indexed: 04/26/2023]  Open
5
Ané C, Fogg J, Allman ES, Baños H, Rhodes JA. ANOMALOUS NETWORKS UNDER THE MULTISPECIES COALESCENT: THEORY AND PREVALENCE. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2023:2023.08.18.553582. [PMID: 37662314 PMCID: PMC10473666 DOI: 10.1101/2023.08.18.553582] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 09/05/2023]
6
Zhang C, Mirarab S. Weighting by Gene Tree Uncertainty Improves Accuracy of Quartet-based Species Trees. Mol Biol Evol 2022;39:6750035. [PMID: 36201617 PMCID: PMC9750496 DOI: 10.1093/molbev/msac215] [Citation(s) in RCA: 24] [Impact Index Per Article: 12.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/08/2022] [Revised: 09/20/2022] [Accepted: 10/03/2022] [Indexed: 01/07/2023]  Open
7
Gatesy J, Springer MS. Phylogenomic Coalescent Analyses of Avian Retroelements Infer Zero-Length Branches at the Base of Neoaves, Emergent Support for Controversial Clades, and Ancient Introgressive Hybridization in Afroaves. Genes (Basel) 2022;13:genes13071167. [PMID: 35885951 PMCID: PMC9324441 DOI: 10.3390/genes13071167] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/23/2022] [Revised: 06/20/2022] [Accepted: 06/21/2022] [Indexed: 01/25/2023]  Open
8
Lamarca AP, Mello B, Schrago CG. The performance of outgroup-free rooting under evolutionary radiations. Mol Phylogenet Evol 2022;169:107434. [PMID: 35143961 DOI: 10.1016/j.ympev.2022.107434] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/22/2021] [Revised: 01/07/2022] [Accepted: 01/25/2022] [Indexed: 11/18/2022]
9
Luo J, Chen J, Guo W, Yang Z, Lim KJ, Wang Z. Reassessment of Annamocarya sinesis (Carya sinensis) Taxonomy through Concatenation and Coalescence Phylogenetic Analysis. PLANTS (BASEL, SWITZERLAND) 2021;11:plants11010052. [PMID: 35009055 PMCID: PMC8747223 DOI: 10.3390/plants11010052] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/17/2021] [Revised: 12/21/2021] [Accepted: 12/22/2021] [Indexed: 05/20/2023]
10
Horvatić S, Malavasi S, Vukić J, Šanda R, Marčić Z, Ćaleta M, Lorenzoni M, Mustafić P, Buj I, Onorato L, Ivić L, Cavraro F, Zanella D. Correlation between acoustic divergence and phylogenetic distance in soniferous European gobiids (Gobiidae; Gobius lineage). PLoS One 2021;16:e0260810. [PMID: 34890403 PMCID: PMC8664166 DOI: 10.1371/journal.pone.0260810] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/04/2021] [Accepted: 11/17/2021] [Indexed: 11/18/2022]  Open
11
Simmons MP, Springer MS, Gatesy J. Gene-tree misrooting drives conflicts in phylogenomic coalescent analyses of palaeognath birds. Mol Phylogenet Evol 2021;167:107344. [PMID: 34748873 DOI: 10.1016/j.ympev.2021.107344] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/13/2021] [Revised: 10/08/2021] [Accepted: 11/02/2021] [Indexed: 10/19/2022]
12
Molloy EK, Gatesy J, Springer MS. Theoretical and practical considerations when using retroelement insertions to estimate species trees in the anomaly zone. Syst Biol 2021;71:721-740. [PMID: 34677617 DOI: 10.1093/sysbio/syab086] [Citation(s) in RCA: 9] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/02/2020] [Accepted: 10/11/2021] [Indexed: 11/13/2022]  Open
13
Arcila D, Hughes LC, Meléndez-Vazquez F, Baldwin CC, White W, Carpenter K, Williams JT, Santos MD, Pogonoski J, Miya M, Ortí G, Betancur-R R. Testing the utility of alternative metrics of branch support to address the ancient evolutionary radiation of tunas, stromateoids, and allies (Teleostei: Pelagiaria). Syst Biol 2021;70:1123-1144. [PMID: 33783539 DOI: 10.1093/sysbio/syab018] [Citation(s) in RCA: 10] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/23/2021] [Accepted: 03/13/2021] [Indexed: 12/19/2022]  Open
14
Collapsing dubiously resolved gene-tree branches in phylogenomic coalescent analyses. Mol Phylogenet Evol 2021;158:107092. [PMID: 33545272 DOI: 10.1016/j.ympev.2021.107092] [Citation(s) in RCA: 17] [Impact Index Per Article: 5.7] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/10/2020] [Revised: 12/30/2020] [Accepted: 01/28/2021] [Indexed: 01/15/2023]
15
Jiang X, Edwards SV, Liu L. The Multispecies Coalescent Model Outperforms Concatenation Across Diverse Phylogenomic Data Sets. Syst Biol 2021;69:795-812. [PMID: 32011711 PMCID: PMC7302055 DOI: 10.1093/sysbio/syaa008] [Citation(s) in RCA: 35] [Impact Index Per Article: 11.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/01/2019] [Revised: 12/24/2019] [Accepted: 01/02/2020] [Indexed: 11/30/2022]  Open
16
Shen XX, Li Y, Hittinger CT, Chen XX, Rokas A. An investigation of irreproducibility in maximum likelihood phylogenetic inference. Nat Commun 2020;11:6096. [PMID: 33257660 PMCID: PMC7705714 DOI: 10.1038/s41467-020-20005-6] [Citation(s) in RCA: 31] [Impact Index Per Article: 7.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/24/2020] [Accepted: 11/05/2020] [Indexed: 01/09/2023]  Open
17
Zhang X, Sun Y, Landis JB, Lv Z, Shen J, Zhang H, Lin N, Li L, Sun J, Deng T, Sun H, Wang H. Plastome phylogenomic study of Gentianeae (Gentianaceae): widespread gene tree discordance and its association with evolutionary rate heterogeneity of plastid genes. BMC PLANT BIOLOGY 2020;20:340. [PMID: 32680458 PMCID: PMC7368685 DOI: 10.1186/s12870-020-02518-w] [Citation(s) in RCA: 26] [Impact Index Per Article: 6.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/03/2020] [Accepted: 06/24/2020] [Indexed: 05/10/2023]
18
Chan KO, Hutter CR, Wood PL, Grismer LL, Brown RM. Larger, unfiltered datasets are more effective at resolving phylogenetic conflict: Introns, exons, and UCEs resolve ambiguities in Golden-backed frogs (Anura: Ranidae; genus Hylarana). Mol Phylogenet Evol 2020;151:106899. [PMID: 32590046 DOI: 10.1016/j.ympev.2020.106899] [Citation(s) in RCA: 20] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/03/2020] [Revised: 05/18/2020] [Accepted: 06/17/2020] [Indexed: 01/01/2023]
19
Vasilikopoulos A, Misof B, Meusemann K, Lieberz D, Flouri T, Beutel RG, Niehuis O, Wappler T, Rust J, Peters RS, Donath A, Podsiadlowski L, Mayer C, Bartel D, Böhm A, Liu S, Kapli P, Greve C, Jepson JE, Liu X, Zhou X, Aspöck H, Aspöck U. An integrative phylogenomic approach to elucidate the evolutionary history and divergence times of Neuropterida (Insecta: Holometabola). BMC Evol Biol 2020;20:64. [PMID: 32493355 PMCID: PMC7268685 DOI: 10.1186/s12862-020-01631-6] [Citation(s) in RCA: 23] [Impact Index Per Article: 5.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/22/2019] [Accepted: 05/19/2020] [Indexed: 02/07/2023]  Open
20
Perea S, Sousa‐Santos C, Robalo J, Doadrio I. Multilocus phylogeny and systematics of Iberian endemicSqualius(Actinopterygii, Leuciscidae). ZOOL SCR 2020. [DOI: 10.1111/zsc.12420] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
21
Springer MS, Molloy EK, Sloan DB, Simmons MP, Gatesy J. ILS-Aware Analysis of Low-Homoplasy Retroelement Insertions: Inference of Species Trees and Introgression Using Quartets. J Hered 2019;111:147-168. [DOI: 10.1093/jhered/esz076] [Citation(s) in RCA: 23] [Impact Index Per Article: 4.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/13/2019] [Accepted: 12/12/2019] [Indexed: 12/20/2022]  Open
22
Gatesy J, Sloan DB, Warren JM, Baker RH, Simmons MP, Springer MS. Partitioned coalescence support reveals biases in species-tree methods and detects gene trees that determine phylogenomic conflicts. Mol Phylogenet Evol 2019;139:106539. [DOI: 10.1016/j.ympev.2019.106539] [Citation(s) in RCA: 15] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/03/2018] [Revised: 06/10/2019] [Accepted: 06/17/2019] [Indexed: 12/26/2022]
23
Alanjary M, Steinke K, Ziemert N. AutoMLST: an automated web server for generating multi-locus species trees highlighting natural product potential. Nucleic Acids Res 2019;47:W276-W282. [PMID: 30997504 PMCID: PMC6602446 DOI: 10.1093/nar/gkz282] [Citation(s) in RCA: 246] [Impact Index Per Article: 49.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/07/2019] [Revised: 03/29/2019] [Accepted: 04/10/2019] [Indexed: 12/31/2022]  Open
24
Simmons MP, Sloan DB, Springer MS, Gatesy J. Gene-wise resampling outperforms site-wise resampling in phylogenetic coalescence analyses. Mol Phylogenet Evol 2019;131:80-92. [DOI: 10.1016/j.ympev.2018.10.001] [Citation(s) in RCA: 24] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/08/2018] [Accepted: 10/01/2018] [Indexed: 01/15/2023]
25
Aharon S, Ballesteros JA, Crawford AR, Friske K, Gainett G, Langford B, Santibáñez-López CE, Ya'aran S, Gavish-Regev E, Sharma PP. The anatomy of an unstable node: a Levantine relict precipitates phylogenomic dissolution of higher-level relationships of the armoured harvestmen (Arachnida: Opiliones: Laniatores). INVERTEBR SYST 2019. [DOI: 10.1071/is19002] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/11/2023]
26
Advances in Computational Methods for Phylogenetic Networks in the Presence of Hybridization. BIOINFORMATICS AND PHYLOGENETICS 2019. [DOI: 10.1007/978-3-030-10837-3_13] [Citation(s) in RCA: 37] [Impact Index Per Article: 7.4] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/12/2022]
27
Anchored hybrid enrichment generated nuclear, plastid and mitochondrial markers resolve the Lepanthes horrida (Orchidaceae: Pleurothallidinae) species complex. Mol Phylogenet Evol 2018;129:27-47. [DOI: 10.1016/j.ympev.2018.07.014] [Citation(s) in RCA: 35] [Impact Index Per Article: 5.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/14/2018] [Revised: 06/25/2018] [Accepted: 07/15/2018] [Indexed: 11/20/2022]
28
Wang X, Lim BK, Ting N, Hu J, Liang Y, Roos C, Yu L. Reconstructing the phylogeny of new world monkeys (platyrrhini): evidence from multiple non-coding loci. Curr Zool 2018;65:579-588. [PMID: 31616489 PMCID: PMC6784508 DOI: 10.1093/cz/zoy072] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/14/2018] [Accepted: 09/12/2018] [Indexed: 11/27/2022]  Open
29
Degnan JH. Modeling Hybridization Under the Network Multispecies Coalescent. Syst Biol 2018;67:786-799. [PMID: 29846734 PMCID: PMC6101600 DOI: 10.1093/sysbio/syy040] [Citation(s) in RCA: 61] [Impact Index Per Article: 10.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/16/2017] [Revised: 05/13/2018] [Accepted: 05/16/2018] [Indexed: 11/13/2022]  Open
30
Sayyari E, Whitfield JB, Mirarab S. Fragmentary Gene Sequences Negatively Impact Gene Tree and Species Tree Reconstruction. Mol Biol Evol 2018;34:3279-3291. [PMID: 29029241 DOI: 10.1093/molbev/msx261] [Citation(s) in RCA: 61] [Impact Index Per Article: 10.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/21/2022]  Open
31
Brower AVZ, Garzón-Orduña IJ. Missing data, clade support and "reticulation": the molecular systematics of Heliconius and related genera (Lepidoptera: Nymphalidae) re-examined. Cladistics 2018;34:151-166. [PMID: 34645081 DOI: 10.1111/cla.12198] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 03/03/2017] [Indexed: 11/30/2022]  Open
32
Vatanparast M, Powell A, Doyle JJ, Egan AN. Targeting legume loci: A comparison of three methods for target enrichment bait design in Leguminosae phylogenomics. APPLICATIONS IN PLANT SCIENCES 2018;6:e1036. [PMID: 29732266 PMCID: PMC5895186 DOI: 10.1002/aps3.1036] [Citation(s) in RCA: 37] [Impact Index Per Article: 6.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/26/2017] [Accepted: 02/22/2018] [Indexed: 05/19/2023]
33
Scornavacca C, Galtier N. Incomplete Lineage Sorting in Mammalian Phylogenomics. Syst Biol 2018;66:112-120. [PMID: 28173480 DOI: 10.1093/sysbio/syw082] [Citation(s) in RCA: 30] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/18/2016] [Revised: 03/25/2016] [Accepted: 09/04/2016] [Indexed: 01/05/2023]  Open
34
Zhong B, Betancur-R R. Expanded Taxonomic Sampling Coupled with Gene Genealogy Interrogation Provides Unambiguous Resolution for the Evolutionary Root of Angiosperms. Genome Biol Evol 2017. [PMCID: PMC5710718 DOI: 10.1093/gbe/evx233] [Citation(s) in RCA: 15] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022]  Open
35
Springer MS, Gatesy J. Pinniped Diphyly and Bat Triphyly: More Homology Errors Drive Conflicts in the Mammalian Tree. J Hered 2017;109:297-307. [DOI: 10.1093/jhered/esx089] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/21/2017] [Accepted: 10/07/2017] [Indexed: 11/14/2022]  Open
36
Ascunce MS, Huguet-Tapia JC, Ortiz-Urquiza A, Keyhani NO, Braun EL, Goss EM. Phylogenomic analysis supports multiple instances of polyphyly in the oomycete peronosporalean lineage. Mol Phylogenet Evol 2017. [DOI: 10.1016/j.ympev.2017.06.013] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/19/2022]
37
Mai U, Sayyari E, Mirarab S. Minimum variance rooting of phylogenetic trees and implications for species tree reconstruction. PLoS One 2017;12:e0182238. [PMID: 28800608 PMCID: PMC5553649 DOI: 10.1371/journal.pone.0182238] [Citation(s) in RCA: 40] [Impact Index Per Article: 5.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/14/2017] [Accepted: 06/25/2017] [Indexed: 12/29/2022]  Open
38
Inferring rooted species trees from unrooted gene trees using approximate Bayesian computation. Mol Phylogenet Evol 2017;116:13-24. [PMID: 28780022 DOI: 10.1016/j.ympev.2017.07.017] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/15/2016] [Revised: 03/26/2017] [Accepted: 07/22/2017] [Indexed: 02/01/2023]
39
Liu Y, Fend SV, Martinsson S, Luo X, Ohtaka A, Erséus C. Multi-locus phylogenetic analysis of the genus Limnodrilus (Annelida: Clitellata: Naididae). Mol Phylogenet Evol 2017;112:244-257. [DOI: 10.1016/j.ympev.2017.04.019] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/22/2016] [Revised: 03/24/2017] [Accepted: 04/20/2017] [Indexed: 12/14/2022]
40
Goloboff PA, Torres A, Arias JS. Weighted parsimony outperforms other methods of phylogenetic inference under models appropriate for morphology. Cladistics 2017;34:407-437. [DOI: 10.1111/cla.12205] [Citation(s) in RCA: 205] [Impact Index Per Article: 29.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 03/22/2017] [Indexed: 11/28/2022]  Open
41
Dupuis J, Brunet B, Bird H, Lumley L, Fagua G, Boyle B, Levesque R, Cusson M, Powell J, Sperling F. Genome-wide SNPs resolve phylogenetic relationships in the North American spruce budworm (Choristoneura fumiferana) species complex. Mol Phylogenet Evol 2017;111:158-168. [DOI: 10.1016/j.ympev.2017.04.001] [Citation(s) in RCA: 26] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/18/2016] [Revised: 02/27/2017] [Accepted: 04/03/2017] [Indexed: 01/02/2023]
42
Chen F, Liu X, Yu C, Chen Y, Tang H, Zhang L. Water lilies as emerging models for Darwin's abominable mystery. HORTICULTURE RESEARCH 2017;4:17051. [PMID: 28979789 PMCID: PMC5626932 DOI: 10.1038/hortres.2017.51] [Citation(s) in RCA: 22] [Impact Index Per Article: 3.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/14/2017] [Revised: 06/30/2017] [Accepted: 07/26/2017] [Indexed: 05/02/2023]
43
Alexander AM, Su Y, Oliveros CH, Olson KV, Travers SL, Brown RM. Genomic data reveals potential for hybridization, introgression, and incomplete lineage sorting to confound phylogenetic relationships in an adaptive radiation of narrow‐mouth frogs. Evolution 2016;71:475-488. [DOI: 10.1111/evo.13133] [Citation(s) in RCA: 34] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/23/2015] [Accepted: 11/07/2016] [Indexed: 12/30/2022]
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Zhao L, Li X, Zhang N, Zhang SD, Yi TS, Ma H, Guo ZH, Li DZ. Phylogenomic analyses of large-scale nuclear genes provide new insights into the evolutionary relationships within the rosids. Mol Phylogenet Evol 2016;105:166-176. [DOI: 10.1016/j.ympev.2016.06.007] [Citation(s) in RCA: 17] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/28/2015] [Revised: 06/06/2016] [Accepted: 06/27/2016] [Indexed: 12/28/2022]
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Sayyari E, Mirarab S. Anchoring quartet-based phylogenetic distances and applications to species tree reconstruction. BMC Genomics 2016;17:783. [PMID: 28185574 PMCID: PMC5123309 DOI: 10.1186/s12864-016-3098-z] [Citation(s) in RCA: 20] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/10/2022]  Open
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Simmons MP. Mutually exclusive phylogenomic inferences at the root of the angiosperms: Amborella is supported as sister and Observed Variability is biased. Cladistics 2016;33:488-512. [DOI: 10.1111/cla.12177] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 09/17/2016] [Indexed: 01/16/2023]  Open
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Gatesy J, Meredith RW, Janecka JE, Simmons MP, Murphy WJ, Springer MS. Resolution of a concatenation/coalescence kerfuffle: partitioned coalescence support and a robust family‐level tree for Mammalia. Cladistics 2016;33:295-332. [DOI: 10.1111/cla.12170] [Citation(s) in RCA: 62] [Impact Index Per Article: 7.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 06/30/2016] [Indexed: 12/14/2022]  Open
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Simmons MP, Gatesy J. Biases of tree-independent-character-subsampling methods. Mol Phylogenet Evol 2016;100:424-443. [DOI: 10.1016/j.ympev.2016.04.022] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/09/2015] [Revised: 03/16/2016] [Accepted: 04/15/2016] [Indexed: 12/21/2022]
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Sayyari E, Mirarab S. Fast Coalescent-Based Computation of Local Branch Support from Quartet Frequencies. Mol Biol Evol 2016;33:1654-68. [PMID: 27189547 PMCID: PMC4915361 DOI: 10.1093/molbev/msw079] [Citation(s) in RCA: 436] [Impact Index Per Article: 54.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022]  Open
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Morrison DA. Genealogies: Pedigrees and Phylogenies are Reticulating Networks Not Just Divergent Trees. Evol Biol 2016. [DOI: 10.1007/s11692-016-9376-5] [Citation(s) in RCA: 50] [Impact Index Per Article: 6.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/01/2023]
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