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For: San Mauro D, Gower DJ, Massingham T, Wilkinson M, Zardoya R, Cotton JA. Experimental design in caecilian systematics: phylogenetic information of mitochondrial genomes and nuclear rag1. Syst Biol 2009;58:425-38. [PMID: 20525595 DOI: 10.1093/sysbio/syp043] [Citation(s) in RCA: 24] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/26/2023]  Open
Number Cited by Other Article(s)
1
Cheung K, Rollins LA, Hammond JM, Barton K, Ferguson JM, Eyck HJF, Shine R, Edwards RJ. Repeat-Rich Regions Cause False-Positive Detection of NUMTs: A Case Study in Amphibians Using an Improved Cane Toad Reference Genome. Genome Biol Evol 2024;16:evae246. [PMID: 39548850 PMCID: PMC11606642 DOI: 10.1093/gbe/evae246] [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: 07/11/2024] [Revised: 10/08/2024] [Accepted: 11/04/2024] [Indexed: 11/18/2024]  Open
2
Mackiewicz P, Urantówka AD, Kroczak A, Mackiewicz D. Resolving Phylogenetic Relationships within Passeriformes Based on Mitochondrial Genes and Inferring the Evolution of Their Mitogenomes in Terms of Duplications. Genome Biol Evol 2019;11:2824-2849. [PMID: 31580435 PMCID: PMC6795242 DOI: 10.1093/gbe/evz209] [Citation(s) in RCA: 18] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 09/30/2019] [Indexed: 12/29/2022]  Open
3
Gates DJ, Pilson D, Smith SD. Filtering of target sequence capture individuals facilitates species tree construction in the plant subtribe Iochrominae (Solanaceae). Mol Phylogenet Evol 2018;123:26-34. [DOI: 10.1016/j.ympev.2018.02.002] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/13/2017] [Revised: 01/30/2018] [Accepted: 02/01/2018] [Indexed: 10/18/2022]
4
Deichmann JL, Mulcahy DG, Vanthomme H, Tobi E, Wynn AH, Zimkus BM, McDiarmid RW. How many species and under what names? Using DNA barcoding and GenBank data for west Central African amphibian conservation. PLoS One 2017;12:e0187283. [PMID: 29131846 PMCID: PMC5683629 DOI: 10.1371/journal.pone.0187283] [Citation(s) in RCA: 20] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/15/2016] [Accepted: 09/06/2017] [Indexed: 11/19/2022]  Open
5
Urantowka AD, Kroczak A, Mackiewicz P. The influence of molecular markers and methods on inferring the phylogenetic relationships between the representatives of the Arini (parrots, Psittaciformes), determined on the basis of their complete mitochondrial genomes. BMC Evol Biol 2017;17:166. [PMID: 28705202 PMCID: PMC5513162 DOI: 10.1186/s12862-017-1012-1] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/03/2016] [Accepted: 07/04/2017] [Indexed: 01/28/2023]  Open
6
Wise MJ. dCITE: Measuring Necessary Cladistic Information Can Help You Reduce Polytomy Artefacts in Trees. PLoS One 2016;11:e0166991. [PMID: 27898695 PMCID: PMC5127522 DOI: 10.1371/journal.pone.0166991] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/09/2016] [Accepted: 11/07/2016] [Indexed: 11/19/2022]  Open
7
Maddock ST, Briscoe AG, Wilkinson M, Waeschenbach A, San Mauro D, Day JJ, Littlewood DTJ, Foster PG, Nussbaum RA, Gower DJ. Next-Generation Mitogenomics: A Comparison of Approaches Applied to Caecilian Amphibian Phylogeny. PLoS One 2016;11:e0156757. [PMID: 27280454 PMCID: PMC4900593 DOI: 10.1371/journal.pone.0156757] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/10/2015] [Accepted: 05/19/2016] [Indexed: 01/06/2023]  Open
8
Lewis PO, Chen MH, Kuo L, Lewis LA, Fučíková K, Neupane S, Wang YB, Shi D. Estimating Bayesian Phylogenetic Information Content. Syst Biol 2016;65:1009-1023. [PMID: 27155008 PMCID: PMC5066063 DOI: 10.1093/sysbio/syw042] [Citation(s) in RCA: 19] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/04/2016] [Revised: 04/15/2016] [Accepted: 05/01/2016] [Indexed: 11/13/2022]  Open
9
Collins RA, Britz R, Rüber L. Phylogenetic systematics of leaffishes (Teleostei: Polycentridae, Nandidae). J ZOOL SYST EVOL RES 2015. [DOI: 10.1111/jzs.12103] [Citation(s) in RCA: 16] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
10
San Mauro D, Gower DJ, Müller H, Loader SP, Zardoya R, Nussbaum RA, Wilkinson M. Life-history evolution and mitogenomic phylogeny of caecilian amphibians. Mol Phylogenet Evol 2014;73:177-89. [PMID: 24480323 DOI: 10.1016/j.ympev.2014.01.009] [Citation(s) in RCA: 63] [Impact Index Per Article: 5.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/29/2013] [Revised: 01/13/2014] [Accepted: 01/16/2014] [Indexed: 11/27/2022]
11
Havird JC, Santos SR. Performance of single and concatenated sets of mitochondrial genes at inferring metazoan relationships relative to full mitogenome data. PLoS One 2014;9:e84080. [PMID: 24454717 PMCID: PMC3891902 DOI: 10.1371/journal.pone.0084080] [Citation(s) in RCA: 31] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/26/2013] [Accepted: 11/11/2013] [Indexed: 12/04/2022]  Open
12
Pedraza-Lara C, Doadrio I, Breinholt JW, Crandall KA. Phylogeny and evolutionary patterns in the Dwarf crayfish subfamily (Decapoda: Cambarellinae). PLoS One 2012;7:e48233. [PMID: 23155379 PMCID: PMC3498282 DOI: 10.1371/journal.pone.0048233] [Citation(s) in RCA: 18] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/22/2011] [Accepted: 09/27/2012] [Indexed: 11/18/2022]  Open
13
Weisrock DW. Concordance analysis in mitogenomic phylogenetics. Mol Phylogenet Evol 2012;65:194-202. [DOI: 10.1016/j.ympev.2012.06.003] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/17/2012] [Revised: 05/22/2012] [Accepted: 06/06/2012] [Indexed: 10/28/2022]
14
Agorreta A, Rüber L. A standardized reanalysis of molecular phylogenetic hypotheses of Gobioidei. SYST BIODIVERS 2012. [DOI: 10.1080/14772000.2012.699477] [Citation(s) in RCA: 17] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/28/2022]
15
San Mauro D, Gower DJ, Cotton JA, Zardoya R, Wilkinson M, Massingham T. Experimental Design in Phylogenetics: Testing Predictions from Expected Information. Syst Biol 2012;61:661-74. [DOI: 10.1093/sysbio/sys028] [Citation(s) in RCA: 11] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/15/2022]  Open
16
Alexander Pyron R, Wiens JJ. A large-scale phylogeny of Amphibia including over 2800 species, and a revised classification of extant frogs, salamanders, and caecilians. Mol Phylogenet Evol 2011;61:543-83. [DOI: 10.1016/j.ympev.2011.06.012] [Citation(s) in RCA: 936] [Impact Index Per Article: 66.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/07/2011] [Revised: 06/10/2011] [Accepted: 06/12/2011] [Indexed: 11/27/2022]
17
Fisher-Reid MC, Wiens JJ. What are the consequences of combining nuclear and mitochondrial data for phylogenetic analysis? Lessons from Plethodon salamanders and 13 other vertebrate clades. BMC Evol Biol 2011;11:300. [PMID: 21995558 PMCID: PMC3203092 DOI: 10.1186/1471-2148-11-300] [Citation(s) in RCA: 72] [Impact Index Per Article: 5.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/25/2011] [Accepted: 10/13/2011] [Indexed: 11/15/2022]  Open
18
Gower DJ, Mauro DS, Giri V, Bhatta G, Govindappa V, Kotharambath R, Oommen OV, Fatih FA, Mackenzie-Dodds JA, Nussbaum RA, Biju S, Shouche YS, Wilkinson M. Molecular systematics of caeciliid caecilians (Amphibia: Gymnophiona) of the Western Ghats, India. Mol Phylogenet Evol 2011;59:698-707. [DOI: 10.1016/j.ympev.2011.03.002] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/13/2010] [Revised: 02/28/2011] [Accepted: 03/02/2011] [Indexed: 10/18/2022]
19
Doherty-Bone TM, Ndifon RK, San Mauro D, Wilkinson M, LeGrand GN, Gower DJ. Systematics and ecology of the caecilianCrotaphatrema lamottei(Nussbaum) (Amphibia: Gymnophiona: Scolecomorphidae). J NAT HIST 2011. [DOI: 10.1080/00222933.2010.535921] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/18/2022]
20
Irisarri I, San Mauro D, Green DM, Zardoya R. The complete mitochondrial genome of the relict frog Leiopelma archeyi: insights into the root of the frog Tree of Life. ACTA ACUST UNITED AC 2011;21:173-82. [PMID: 20958226 DOI: 10.3109/19401736.2010.513973] [Citation(s) in RCA: 28] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/13/2022]
21
A multilocus timescale for the origin of extant amphibians. Mol Phylogenet Evol 2010;56:554-61. [DOI: 10.1016/j.ympev.2010.04.019] [Citation(s) in RCA: 84] [Impact Index Per Article: 5.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/04/2009] [Revised: 04/06/2010] [Accepted: 04/13/2010] [Indexed: 11/15/2022]
22
Molecular systematics: A synthesis of the common methods and the state of knowledge. Cell Mol Biol Lett 2010;15:311-41. [PMID: 20213503 PMCID: PMC6275913 DOI: 10.2478/s11658-010-0010-8] [Citation(s) in RCA: 41] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/16/2009] [Accepted: 03/01/2010] [Indexed: 11/21/2022]  Open
23
Klopfstein S, Kropf C, Quicke DLJ. An evaluation of phylogenetic informativeness profiles and the molecular phylogeny of diplazontinae (Hymenoptera, Ichneumonidae). Syst Biol 2010;59:226-41. [PMID: 20525632 DOI: 10.1093/sysbio/syp105] [Citation(s) in RCA: 53] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/13/2022]  Open
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