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For: Petersen M, Meusemann K, Donath A, Dowling D, Liu S, Peters RS, Podsiadlowski L, Vasilikopoulos A, Zhou X, Misof B, Niehuis O. Orthograph: a versatile tool for mapping coding nucleotide sequences to clusters of orthologous genes. BMC Bioinformatics 2017;18:111. [PMID: 28209129 PMCID: PMC5312442 DOI: 10.1186/s12859-017-1529-8] [Citation(s) in RCA: 71] [Impact Index Per Article: 10.1] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/25/2016] [Accepted: 02/06/2017] [Indexed: 01/16/2023]  Open
Number Cited by Other Article(s)
1
Li Y, Moritz C, Brennan IG, Zwick A, Nicholls J, Grealy A, Slipinski A. Evolution across the adaptive landscape in a hyperdiverse beetle radiation. Curr Biol 2024:S0960-9822(24)00898-4. [PMID: 39067451 DOI: 10.1016/j.cub.2024.06.080] [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: 04/02/2024] [Revised: 05/30/2024] [Accepted: 06/28/2024] [Indexed: 07/30/2024]
2
Huang YH, Sun YF, Li H, Li HS, Pang H. PhyloAln: A Convenient Reference-Based Tool to Align Sequences and High-Throughput Reads for Phylogeny and Evolution in the Omic Era. Mol Biol Evol 2024;41:msae150. [PMID: 39041199 DOI: 10.1093/molbev/msae150] [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: 02/14/2024] [Revised: 05/15/2024] [Accepted: 07/16/2024] [Indexed: 07/24/2024]  Open
3
Cerretti P, Yan L, Narayanan Kutty S, Szpila K, Nania D, Tintea R, Mei M, Pape T. Phylogenomics resolves long-standing questions about the affinities of an endangered Corsican endemic fly. JOURNAL OF INSECT SCIENCE (ONLINE) 2024;24:9. [PMID: 39052426 PMCID: PMC11271022 DOI: 10.1093/jisesa/ieae073] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/11/2024] [Revised: 05/25/2024] [Accepted: 06/24/2024] [Indexed: 07/27/2024]
4
Frandsen PB, Holzenthal RW, Espeland M, Breinholt J, Thomas Thorpe JA, Simon S, Kawahara AY, Plotkin D, Hotaling S, Li Y, Nelson CR, Niehuis O, Mayer C, Podsiadlowski L, Donath A, Misof B, Moriarty Lemmon E, Lemmon A, Morse JC, Liu S, Pauls SU, Zhou X. Phylogenomics recovers multiple origins of portable case making in caddisflies (Insecta: Trichoptera), nature's underwater architects. Proc Biol Sci 2024;291:20240514. [PMID: 38955232 DOI: 10.1098/rspb.2024.0514] [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: 03/05/2024] [Accepted: 06/10/2024] [Indexed: 07/04/2024]  Open
5
Dietz L, Mayer C, Stolle E, Eberle J, Misof B, Podsiadlowski L, Niehuis O, Ahrens D. Metazoa-level USCOs as markers in species delimitation and classification. Mol Ecol Resour 2024;24:e13921. [PMID: 38146909 DOI: 10.1111/1755-0998.13921] [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: 10/15/2023] [Revised: 12/06/2023] [Accepted: 12/13/2023] [Indexed: 12/27/2023]
6
Li X, Breinholt JW, Martinez JI, Keegan K, Ellis EA, Homziak NT, Zwick A, Storer CG, McKenna D, Kawahara AY. Large-scale genomic data reveal the phylogeny and evolution of owlet moths (Noctuoidea). Cladistics 2024;40:21-33. [PMID: 37787424 DOI: 10.1111/cla.12559] [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: 04/21/2023] [Revised: 08/24/2023] [Accepted: 08/28/2023] [Indexed: 10/04/2023]  Open
7
Soghigian J, Sither C, Justi SA, Morinaga G, Cassel BK, Vitek CJ, Livdahl T, Xia S, Gloria-Soria A, Powell JR, Zavortink T, Hardy CM, Burkett-Cadena ND, Reeves LE, Wilkerson RC, Dunn RR, Yeates DK, Sallum MA, Byrd BD, Trautwein MD, Linton YM, Reiskind MH, Wiegmann BM. Phylogenomics reveals the history of host use in mosquitoes. Nat Commun 2023;14:6252. [PMID: 37803007 PMCID: PMC10558525 DOI: 10.1038/s41467-023-41764-y] [Citation(s) in RCA: 6] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/25/2023] [Accepted: 09/08/2023] [Indexed: 10/08/2023]  Open
8
Flury JM, Meusemann K, Martin S, Hilgers L, Spanke T, Böhne A, Herder F, Mokodongan DF, Altmüller J, Wowor D, Misof B, Nolte AW, Schwarzer J. Potential Contribution of Ancient Introgression to the Evolution of a Derived Reproductive Strategy in Ricefishes. Genome Biol Evol 2023;15:evad138. [PMID: 37493080 PMCID: PMC10465105 DOI: 10.1093/gbe/evad138] [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: 07/05/2022] [Revised: 06/28/2023] [Accepted: 07/13/2023] [Indexed: 07/27/2023]  Open
9
Feng T, Pucker B, Kuang T, Song B, Yang Y, Lin N, Zhang H, Moore MJ, Brockington SF, Wang Q, Deng T, Wang H, Sun H. The genome of the glasshouse plant noble rhubarb (Rheum nobile) provides a window into alpine adaptation. Commun Biol 2023;6:706. [PMID: 37429977 DOI: 10.1038/s42003-023-05044-1] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/04/2022] [Accepted: 06/14/2023] [Indexed: 07/12/2023]  Open
10
Wang YH, Luan YX, Luo JY, Men Y, Engel MS, Damgaard J, Khila A, Chen PP, Figueiredo Moreira FF, Rafael JA, Xie Q. 300 Million years of coral treaders (Insecta: Heteroptera: Hermatobatidae) back to the ocean in the phylogenetic context of Arthropoda. Proc Biol Sci 2023;290:20230855. [PMID: 37357866 PMCID: PMC10291715 DOI: 10.1098/rspb.2023.0855] [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: 12/13/2022] [Accepted: 06/06/2023] [Indexed: 06/27/2023]  Open
11
Liu JL, Zhang JW, Han W, Wang YS, He SL, Wang ZQ. Advances in the understanding of Blattodea evolution: Insights from phylotranscriptomics and spermathecae. Mol Phylogenet Evol 2023;182:107753. [PMID: 36898488 DOI: 10.1016/j.ympev.2023.107753] [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: 12/10/2022] [Revised: 03/03/2023] [Accepted: 03/03/2023] [Indexed: 03/12/2023]
12
Xuan JL, Scheffer SJ, Lewis M, Cassel BK, Liu WX, Wiegmann BM. The phylogeny and divergence times of leaf-mining flies (Diptera: Agromyzidae) from anchored phylogenomics. Mol Phylogenet Evol 2023;184:107778. [PMID: 37030415 DOI: 10.1016/j.ympev.2023.107778] [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: 10/17/2022] [Revised: 02/24/2023] [Accepted: 03/31/2023] [Indexed: 04/10/2023]
13
Watanabe T, Kure A, Horiike T. OrthoPhy: A Program to Construct Ortholog Data Sets Using Taxonomic Information. Genome Biol Evol 2023;15:7044703. [PMID: 36799928 PMCID: PMC9991595 DOI: 10.1093/gbe/evad026] [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: 06/09/2022] [Revised: 01/30/2023] [Accepted: 02/13/2023] [Indexed: 02/18/2023]  Open
14
Ragionieri L, Zúñiga-Reinoso Á, Bläser M, Predel R. Phylogenomics of darkling beetles (Coleoptera: Tenebrionidae) from the Atacama Desert. PeerJ 2023;11:e14848. [PMID: 36855434 PMCID: PMC9968461 DOI: 10.7717/peerj.14848] [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: 10/04/2022] [Accepted: 01/12/2023] [Indexed: 02/25/2023]  Open
15
Winkler IS, Kirk-Spriggs AH, Bayless KM, Soghigian J, Meier R, Pape T, Yeates DK, Carvalho AB, Copeland RS, Wiegmann BM. Phylogenetic resolution of the fly superfamily Ephydroidea-Molecular systematics of the enigmatic and diverse relatives of Drosophilidae. PLoS One 2022;17:e0274292. [PMID: 36197946 PMCID: PMC9534441 DOI: 10.1371/journal.pone.0274292] [Citation(s) in RCA: 5] [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: 02/23/2022] [Accepted: 08/26/2022] [Indexed: 11/05/2022]  Open
16
Lozano-Fernandez J. A Practical Guide to Design and Assess a Phylogenomic Study. Genome Biol Evol 2022;14:evac129. [PMID: 35946263 PMCID: PMC9452790 DOI: 10.1093/gbe/evac129] [Citation(s) in RCA: 8] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 08/03/2022] [Indexed: 11/13/2022]  Open
17
Reconstruction of the rRNA Sequences of LUCA, with Bioinformatic Implication of the Local Similarities Shared by Them. BIOLOGY 2022;11:biology11060837. [PMID: 35741358 PMCID: PMC9219793 DOI: 10.3390/biology11060837] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 04/05/2022] [Revised: 05/19/2022] [Accepted: 05/23/2022] [Indexed: 11/17/2022]
18
Jin M, Shin S, Ashman LG, Leschen RAB, Zwick A, de Keyzer R, McKenna DD, Ślipiński A. Phylogenomics resolves timing and patterns in the evolution of Australasian Cerambycinae (Coleoptera: Cerambycidae), and reveals new insights into the subfamily-level classification and historical biogeography of longhorn beetles. Mol Phylogenet Evol 2022;172:107486. [PMID: 35469917 DOI: 10.1016/j.ympev.2022.107486] [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: 08/16/2021] [Revised: 02/12/2022] [Accepted: 04/05/2022] [Indexed: 11/25/2022]
19
Ye F, Kment P, Rédei D, Luo JY, Wang YH, Kuechler SM, Zhang WW, Chen PP, Wu HY, Wu YZ, Sun XY, Ding L, Wang YR, Xie Q. Diversification of the phytophagous lineages of true bugs (Insecta: Hemiptera: Heteroptera) shortly after that of the flowering plants. Cladistics 2022;38:403-428. [PMID: 35349192 DOI: 10.1111/cla.12501] [Citation(s) in RCA: 13] [Impact Index Per Article: 6.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/08/2021] [Revised: 02/20/2022] [Accepted: 02/22/2022] [Indexed: 12/20/2022]  Open
20
Hou Z, Ma X, Shi X, Li X, Yang L, Xiao S, De Clerck O, Leliaert F, Zhong B. Phylotranscriptomic insights into a Mesoproterozoic-Neoproterozoic origin and early radiation of green seaweeds (Ulvophyceae). Nat Commun 2022;13:1610. [PMID: 35318329 PMCID: PMC8941102 DOI: 10.1038/s41467-022-29282-9] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/28/2021] [Accepted: 03/09/2022] [Indexed: 01/09/2023]  Open
21
Karmeinski D, Meusemann K, Goodheart JA, Schroedl M, Martynov A, Korshunova T, Wägele H, Donath A. Transcriptomics provides a robust framework for the relationships of the major clades of cladobranch sea slugs (Mollusca, Gastropoda, Heterobranchia), but fails to resolve the position of the enigmatic genus Embletonia. BMC Ecol Evol 2021;21:226. [PMID: 34963462 PMCID: PMC8895541 DOI: 10.1186/s12862-021-01944-0] [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: 09/29/2020] [Accepted: 11/23/2021] [Indexed: 11/24/2022]  Open
22
Motyka M, Kusy D, Bocek M, Bilkova R, Bocak L. Phylogenomic and mitogenomic data can accelerate inventorying of tropical beetles during the current biodiversity crisis. eLife 2021;10:71895. [PMID: 34927586 PMCID: PMC8798050 DOI: 10.7554/elife.71895] [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: 07/02/2021] [Accepted: 12/18/2021] [Indexed: 11/13/2022]  Open
23
Kohli M, Letsch H, Greve C, Béthoux O, Deregnaucourt I, Liu S, Zhou X, Donath A, Mayer C, Podsiadlowski L, Gunkel S, Machida R, Niehuis O, Rust J, Wappler T, Yu X, Misof B, Ware J. Evolutionary history and divergence times of Odonata (dragonflies and damselflies) revealed through transcriptomics. iScience 2021;24:103324. [PMID: 34805787 PMCID: PMC8586788 DOI: 10.1016/j.isci.2021.103324] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/02/2020] [Revised: 05/14/2021] [Accepted: 10/19/2021] [Indexed: 11/22/2022]  Open
24
Lu H, Chen L, Pan X, Yao Y, Zhang H, Zhu X, Lou X, Zhu C, Wang J, Li L, Wu Z. Lactitol Supplementation Modulates Intestinal Microbiome in Liver Cirrhotic Patients. Front Med (Lausanne) 2021;8:762930. [PMID: 34722597 PMCID: PMC8551616 DOI: 10.3389/fmed.2021.762930] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/23/2021] [Accepted: 09/16/2021] [Indexed: 12/12/2022]  Open
25
Aspergillus sp. A31 and Curvularia geniculata P1 mitigate mercury toxicity to Oryza sativa L. Arch Microbiol 2021;203:5345-5361. [PMID: 34387704 DOI: 10.1007/s00203-021-02481-6] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/17/2021] [Revised: 07/05/2021] [Accepted: 07/07/2021] [Indexed: 12/29/2022]
26
Yan L, Pape T, Meusemann K, Kutty SN, Meier R, Bayless KM, Zhang D. Monophyletic blowflies revealed by phylogenomics. BMC Biol 2021;19:230. [PMID: 34706743 PMCID: PMC8555136 DOI: 10.1186/s12915-021-01156-4] [Citation(s) in RCA: 12] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/07/2020] [Accepted: 09/23/2021] [Indexed: 12/24/2022]  Open
27
Yan L, Buenaventura E, Pape T, Narayanan Kutty S, Bayless KM, Zhang D. A phylotranscriptomic framework for flesh fly evolution (Diptera, Calyptratae, Sarcophagidae). Cladistics 2021;37:540-558. [PMID: 34570937 DOI: 10.1111/cla.12449] [Citation(s) in RCA: 12] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 11/23/2020] [Indexed: 11/28/2022]  Open
28
Stringer DN, Bertozzi T, Meusemann K, Delean S, Guzik MT, Tierney SM, Mayer C, Cooper SJB, Javidkar M, Zwick A, Austin AD. Development and evaluation of a custom bait design based on 469 single-copy protein-coding genes for exon capture of isopods (Philosciidae: Haloniscus). PLoS One 2021;16:e0256861. [PMID: 34534224 PMCID: PMC8448321 DOI: 10.1371/journal.pone.0256861] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/03/2020] [Accepted: 08/17/2021] [Indexed: 12/02/2022]  Open
29
Li X, Teasdale LC, Bayless KM, Ellis AG, Wiegmann BM, Lamas CJE, Lambkin CL, Evenhuis NL, Nicholls JA, Hartley D, Shin S, Trautwein M, Zwick A, Lessard BD, Yeates DK. Phylogenomics reveals accelerated late Cretaceous diversification of bee flies (Diptera: Bombyliidae). Cladistics 2021;37:276-297. [PMID: 34478201 DOI: 10.1111/cla.12436] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/23/2019] [Revised: 07/07/2020] [Accepted: 08/18/2020] [Indexed: 02/06/2023]  Open
30
Fifty million years of beetle evolution along the Antarctic Polar Front. Proc Natl Acad Sci U S A 2021;118:2017384118. [PMID: 34108239 PMCID: PMC8214695 DOI: 10.1073/pnas.2017384118] [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] [Indexed: 11/18/2022]  Open
31
Douglas HB, Kundrata R, Brunke AJ, Escalona HE, Chapados JT, Eyres J, Richter R, Savard K, Ślipiński A, McKenna D, Dettman JR. Anchored Phylogenomics, Evolution and Systematics of Elateridae: Are All Bioluminescent Elateroidea Derived Click Beetles? BIOLOGY 2021;10:biology10060451. [PMID: 34063961 PMCID: PMC8224040 DOI: 10.3390/biology10060451] [Citation(s) in RCA: 21] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 04/24/2021] [Revised: 05/17/2021] [Accepted: 05/18/2021] [Indexed: 12/21/2022]
32
Cheon S, Zhang J, Park C. Is Phylotranscriptomics as Reliable as Phylogenomics? Mol Biol Evol 2021;37:3672-3683. [PMID: 32658973 PMCID: PMC7743905 DOI: 10.1093/molbev/msaa181] [Citation(s) in RCA: 33] [Impact Index Per Article: 11.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/12/2022]  Open
33
Li X, Hou Z, Xu C, Shi X, Yang L, Lewis LA, Zhong B. Large Phylogenomic Data sets Reveal Deep Relationships and Trait Evolution in Chlorophyte Green Algae. Genome Biol Evol 2021;13:6265471. [PMID: 33950183 PMCID: PMC8271138 DOI: 10.1093/gbe/evab101] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 05/04/2021] [Indexed: 12/01/2022]  Open
34
Su D, Yang L, Shi X, Ma X, Zhou X, Hedges SB, Zhong B. Large-Scale Phylogenomic Analyses Reveal the Monophyly of Bryophytes and Neoproterozoic Origin of Land Plants. Mol Biol Evol 2021;38:3332-3344. [PMID: 33871608 PMCID: PMC8321542 DOI: 10.1093/molbev/msab106] [Citation(s) in RCA: 35] [Impact Index Per Article: 11.7] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/06/2023]  Open
35
Knyshov A, Gordon ERL, Weirauch C. New alignment-based sequence extraction software (ALiBaSeq) and its utility for deep level phylogenetics. PeerJ 2021;9:e11019. [PMID: 33850647 PMCID: PMC8019319 DOI: 10.7717/peerj.11019] [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: 09/07/2020] [Accepted: 02/06/2021] [Indexed: 01/03/2023]  Open
36
Feldbauer R, Gosch L, Lüftinger L, Hyden P, Flexer A, Rattei T. DeepNOG: fast and accurate protein orthologous group assignment. Bioinformatics 2021;36:5304-5312. [PMID: 33367584 PMCID: PMC8016488 DOI: 10.1093/bioinformatics/btaa1051] [Citation(s) in RCA: 12] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/24/2020] [Revised: 12/02/2020] [Accepted: 12/10/2020] [Indexed: 11/30/2022]  Open
37
Scossa F, Fernie AR. Ancestral sequence reconstruction - An underused approach to understand the evolution of gene function in plants? Comput Struct Biotechnol J 2021;19:1579-1594. [PMID: 33868595 PMCID: PMC8039532 DOI: 10.1016/j.csbj.2021.03.008] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/03/2021] [Revised: 03/04/2021] [Accepted: 03/06/2021] [Indexed: 02/06/2023]  Open
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Andrade Justi S, Soghigian J, Pecor DB, Caicedo-Quiroga L, Rutvisuttinunt W, Li T, Stevens L, Dorn PL, Wiegmann B, Linton YM. From e-voucher to genomic data: Preserving archive specimens as demonstrated with medically important mosquitoes (Diptera: Culicidae) and kissing bugs (Hemiptera: Reduviidae). PLoS One 2021;16:e0247068. [PMID: 33630885 PMCID: PMC7906454 DOI: 10.1371/journal.pone.0247068] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/27/2020] [Accepted: 01/29/2021] [Indexed: 12/26/2022]  Open
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Bayless KM, Trautwein MD, Meusemann K, Shin S, Petersen M, Donath A, Podsiadlowski L, Mayer C, Niehuis O, Peters RS, Meier R, Kutty SN, Liu S, Zhou X, Misof B, Yeates DK, Wiegmann BM. Beyond Drosophila: resolving the rapid radiation of schizophoran flies with phylotranscriptomics. BMC Biol 2021;19:23. [PMID: 33557827 PMCID: PMC7871583 DOI: 10.1186/s12915-020-00944-8] [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: 05/20/2020] [Accepted: 12/17/2020] [Indexed: 01/15/2023]  Open
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Schoville SD, Simon S, Bai M, Beethem Z, Dudko RY, Eberhard MJB, Frandsen PB, Küpper SC, Machida R, Verheij M, Willadsen PC, Zhou X, Wipfler B. Comparative transcriptomics of ice-crawlers demonstrates cold specialization constrains niche evolution in a relict lineage. Evol Appl 2021;14:360-382. [PMID: 33664782 PMCID: PMC7896716 DOI: 10.1111/eva.13120] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/11/2020] [Revised: 07/25/2020] [Accepted: 08/17/2020] [Indexed: 12/26/2022]  Open
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Maletti S, Niehuis O, Mayer C, Sann M, Klopfstein S, Nottebrock G, Baur H, Peters RS. Phylogeny, taxonomics, and ovipositor length variation of the Pteromalus albipennis species group (Hymenoptera: Chalcidoidea: Pteromalidae: Pteromalinae). J ZOOL SYST EVOL RES 2021. [DOI: 10.1111/jzs.12433] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/01/2022]
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Li HS, Tang XF, Huang YH, Xu ZY, Chen ML, Du XY, Qiu BY, Chen PT, Zhang W, Ślipiński A, Escalona HE, Waterhouse RM, Zwick A, Pang H. Horizontally acquired antibacterial genes associated with adaptive radiation of ladybird beetles. BMC Biol 2021;19:7. [PMID: 33446206 PMCID: PMC7807722 DOI: 10.1186/s12915-020-00945-7] [Citation(s) in RCA: 7] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/19/2020] [Accepted: 12/22/2020] [Indexed: 01/12/2023]  Open
43
Szucsich NU, Bartel D, Blanke A, Böhm A, Donath A, Fukui M, Grove S, Liu S, Macek O, Machida R, Misof B, Nakagaki Y, Podsiadlowski L, Sekiya K, Tomizuka S, Von Reumont BM, Waterhouse RM, Walzl M, Meng G, Zhou X, Pass G, Meusemann K. Four myriapod relatives - but who are sisters? No end to debates on relationships among the four major myriapod subgroups. BMC Evol Biol 2020;20:144. [PMID: 33148176 PMCID: PMC7640414 DOI: 10.1186/s12862-020-01699-0] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/16/2020] [Accepted: 09/30/2020] [Indexed: 11/20/2022]  Open
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Song H, Béthoux O, Shin S, Donath A, Letsch H, Liu S, McKenna DD, Meng G, Misof B, Podsiadlowski L, Zhou X, Wipfler B, Simon S. Phylogenomic analysis sheds light on the evolutionary pathways towards acoustic communication in Orthoptera. Nat Commun 2020;11:4939. [PMID: 33009390 PMCID: PMC7532154 DOI: 10.1038/s41467-020-18739-4] [Citation(s) in RCA: 41] [Impact Index Per Article: 10.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/10/2020] [Accepted: 09/11/2020] [Indexed: 01/01/2023]  Open
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Measuring Genome Sizes Using Read-Depth, k-mers, and Flow Cytometry: Methodological Comparisons in Beetles (Coleoptera). G3-GENES GENOMES GENETICS 2020;10:3047-3060. [PMID: 32601059 PMCID: PMC7466995 DOI: 10.1534/g3.120.401028] [Citation(s) in RCA: 53] [Impact Index Per Article: 13.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Indexed: 11/25/2022]
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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
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Phylogenetic tree building in the genomic age. Nat Rev Genet 2020;21:428-444. [PMID: 32424311 DOI: 10.1038/s41576-020-0233-0] [Citation(s) in RCA: 162] [Impact Index Per Article: 40.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 03/20/2020] [Indexed: 01/22/2023]
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Meusemann K, Korb J, Schughart M, Staubach F. No Evidence for Single-Copy Immune-Gene Specific Signals of Selection in Termites. Front Ecol Evol 2020. [DOI: 10.3389/fevo.2020.00026] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/30/2022]  Open
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Zhang Z, Qu C, Yao R, Nie Y, Xu C, Miao J, Zhong B. The Parallel Molecular Adaptations to the Antarctic Cold Environment in Two Psychrophilic Green Algae. Genome Biol Evol 2020;11:1897-1908. [PMID: 31106822 PMCID: PMC6628873 DOI: 10.1093/gbe/evz104] [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] [Accepted: 05/09/2019] [Indexed: 01/02/2023]  Open
50
Phylogenomics reveals the evolutionary timing and pattern of butterflies and moths. Proc Natl Acad Sci U S A 2019;116:22657-22663. [PMID: 31636187 PMCID: PMC6842621 DOI: 10.1073/pnas.1907847116] [Citation(s) in RCA: 169] [Impact Index Per Article: 33.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/19/2023]  Open
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