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For: Wertheim JO, Murrell B, Smith MD, Kosakovsky Pond SL, Scheffler K. RELAX: detecting relaxed selection in a phylogenetic framework. Mol Biol Evol 2014;32:820-32. [PMID: 25540451 DOI: 10.1093/molbev/msu400] [Citation(s) in RCA: 391] [Impact Index Per Article: 39.1] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/12/2022]  Open
Number Cited by Other Article(s)
1
Kitchen SA, Naragon TH, Brückner A, Ladinsky MS, Quinodoz SA, Badroos JM, Viliunas JW, Kishi Y, Wagner JM, Miller DR, Yousefelahiyeh M, Antoshechkin IA, Eldredge KT, Pirro S, Guttman M, Davis SR, Aardema ML, Parker J. The genomic and cellular basis of biosynthetic innovation in rove beetles. Cell 2024:S0092-8674(24)00521-X. [PMID: 38889727 DOI: 10.1016/j.cell.2024.05.012] [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: 06/07/2023] [Revised: 02/29/2024] [Accepted: 05/06/2024] [Indexed: 06/20/2024]
2
Yusuf LH, Lemus YS, Thorpe P, Garcia CM, Ritchie MG. Evidence for gene flow and trait reversal during radiation of Mexican Goodeid fish. Heredity (Edinb) 2024:10.1038/s41437-024-00694-1. [PMID: 38858547 DOI: 10.1038/s41437-024-00694-1] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/06/2023] [Revised: 05/15/2024] [Accepted: 05/16/2024] [Indexed: 06/12/2024]  Open
3
Bennett GM, Kwak Y, Maynard R. Endosymbioses Have Shaped the Evolution of Biological Diversity and Complexity Time and Time Again. Genome Biol Evol 2024;16:evae112. [PMID: 38813885 PMCID: PMC11154151 DOI: 10.1093/gbe/evae112] [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: 04/23/2024] [Revised: 05/17/2024] [Accepted: 05/17/2024] [Indexed: 05/31/2024]  Open
4
Boyette JL, Bell RC, Fujita MK, Thomas KN, Streicher JW, Gower DJ, Schott RK. Diversity and Molecular Evolution of Nonvisual Opsin Genes across Environmental, Developmental, and Morphological Adaptations in Frogs. Mol Biol Evol 2024;41:msae090. [PMID: 38736374 PMCID: PMC11181710 DOI: 10.1093/molbev/msae090] [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: 09/12/2023] [Revised: 05/03/2024] [Accepted: 05/07/2024] [Indexed: 05/14/2024]  Open
5
Selleghin-Veiga G, Magpali L, Picorelli A, Silva FA, Ramos E, Nery MF. Breathing Air and Living Underwater: Molecular Evolution of Genes Related to Antioxidant Response in Cetaceans and Pinnipeds. J Mol Evol 2024;92:300-316. [PMID: 38735005 DOI: 10.1007/s00239-024-10170-3] [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: 05/21/2023] [Accepted: 04/05/2024] [Indexed: 05/13/2024]
6
Drabeck DH, Wiese J, Gilbertson E, Arroyave J, Stiassny MLJ, Alter SE, Borowsky R, Hendrickson DA, Arcila D, McGaugh SE. Gene loss and relaxed selection of plaat1 in vertebrates adapted to low-light environments. Proc Biol Sci 2024;291:20232847. [PMID: 38864338 DOI: 10.1098/rspb.2023.2847] [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: 12/15/2023] [Accepted: 05/03/2024] [Indexed: 06/13/2024]  Open
7
Ding Y, Zou M, Guo B. Genomic signatures associated with recurrent scale loss in cyprinid fish. Integr Zool 2024. [PMID: 38816909 DOI: 10.1111/1749-4877.12851] [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] [Indexed: 06/01/2024]
8
Edwards SV, Cloutier A, Cockburn G, Driver R, Grayson P, Katoh K, Baldwin MW, Sackton TB, Baker AJ. A nuclear genome assembly of an extinct flightless bird, the little bush moa. SCIENCE ADVANCES 2024;10:eadj6823. [PMID: 38781323 DOI: 10.1126/sciadv.adj6823] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/10/2023] [Accepted: 04/17/2024] [Indexed: 05/25/2024]
9
Formaggioni A, Cavalli G, Hamada M, Sakamoto T, Plazzi F, Passamonti M. The Evolution and Characterization of the RNA Interference Pathways in Lophotrochozoa. Genome Biol Evol 2024;16:evae098. [PMID: 38713108 PMCID: PMC11114477 DOI: 10.1093/gbe/evae098] [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: 10/23/2023] [Revised: 04/24/2024] [Accepted: 04/30/2024] [Indexed: 05/08/2024]  Open
10
Nell LA, Weng YM, Phillips JS, Botsch JC, Book KR, Einarsson Á, Ives AR, Schoville SD. Shared Features Underlying Compact Genomes and Extreme Habitat Use in Chironomid Midges. Genome Biol Evol 2024;16:evae086. [PMID: 38662498 PMCID: PMC11076180 DOI: 10.1093/gbe/evae086] [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] [Accepted: 04/21/2024] [Indexed: 05/09/2024]  Open
11
Fields PD, Jalinsky JR, Bankers L, McElroy KE, Sharbrough J, Higgins C, Morgan-Richards M, Boore JL, Neiman M, Logsdon JM. Genome Evolution and Introgression in the New Zealand mud Snails Potamopyrgus estuarinus and Potamopyrgus kaitunuparaoa. Genome Biol Evol 2024;16:evae091. [PMID: 38776329 PMCID: PMC11110935 DOI: 10.1093/gbe/evae091] [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] [Accepted: 04/22/2024] [Indexed: 05/24/2024]  Open
12
Ewart KM, Ho SYW, Chowdhury AA, Jaya FR, Kinjo Y, Bennett J, Bourguignon T, Rose HA, Lo N. Pervasive relaxed selection in termite genomes. Proc Biol Sci 2024;291:20232439. [PMID: 38772424 DOI: 10.1098/rspb.2023.2439] [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: 10/30/2023] [Accepted: 05/02/2024] [Indexed: 05/23/2024]  Open
13
Herrick J. DNA Damage, Genome Stability, and Adaptation: A Question of Chance or Necessity? Genes (Basel) 2024;15:520. [PMID: 38674454 PMCID: PMC11049855 DOI: 10.3390/genes15040520] [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: 03/17/2024] [Revised: 04/14/2024] [Accepted: 04/18/2024] [Indexed: 04/28/2024]  Open
14
Chen LQ, Li X, Yao X, Li DZ, Barrett C, dePamphilis CW, Yu WB. Variations and reduction of plastome are associated with the evolution of parasitism in Convolvulaceae. PLANT MOLECULAR BIOLOGY 2024;114:40. [PMID: 38622367 DOI: 10.1007/s11103-024-01440-1] [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: 08/18/2023] [Accepted: 03/09/2024] [Indexed: 04/17/2024]
15
York JM, Taylor TN, LaPotin S, Lu Y, Mueller U. Hymenopteran-specific TRPA channel from the Texas leaf cutter ant (Atta texana) is heat and cold activated and expression correlates with environmental temperature. INSECT SCIENCE 2024. [PMID: 38605428 DOI: 10.1111/1744-7917.13364] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/04/2023] [Revised: 03/05/2024] [Accepted: 03/07/2024] [Indexed: 04/13/2024]
16
Lin TD, Rubinstein ND, Fong NL, Smith M, Craft W, Martin-McNulty B, Perry R, Delaney MA, Roy MA, Buffenstein R. Evolution of T cells in the cancer-resistant naked mole-rat. Nat Commun 2024;15:3145. [PMID: 38605005 PMCID: PMC11009300 DOI: 10.1038/s41467-024-47264-x] [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: 04/24/2023] [Accepted: 03/26/2024] [Indexed: 04/13/2024]  Open
17
Zheng W, Gojobori J, Suh A, Satta Y. Different Host-Endogenous Retrovirus Relationships between Mammals and Birds Reflected in Genome-Wide Evolutionary Interaction Patterns. Genome Biol Evol 2024;16:evae065. [PMID: 38527852 PMCID: PMC11005779 DOI: 10.1093/gbe/evae065] [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: 07/28/2023] [Revised: 02/25/2024] [Accepted: 03/21/2024] [Indexed: 03/27/2024]  Open
18
Schott RK, Fujita MK, Streicher JW, Gower DJ, Thomas KN, Loew ER, Bamba Kaya AG, Bittencourt-Silva GB, Guillherme Becker C, Cisneros-Heredia D, Clulow S, Davila M, Firneno TJ, Haddad CFB, Janssenswillen S, Labisko J, Maddock ST, Mahony M, Martins RA, Michaels CJ, Mitchell NJ, Portik DM, Prates I, Roelants K, Roelke C, Tobi E, Woolfolk M, Bell RC. Diversity and Evolution of Frog Visual Opsins: Spectral Tuning and Adaptation to Distinct Light Environments. Mol Biol Evol 2024;41:msae049. [PMID: 38573520 PMCID: PMC10994157 DOI: 10.1093/molbev/msae049] [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: 09/12/2023] [Revised: 02/07/2024] [Accepted: 02/26/2024] [Indexed: 04/05/2024]  Open
19
Wu W, Feng X, Wang N, Shao S, Liu M, Si F, Chen L, Jin C, Xu S, Guo Z, Zhong C, Shi S, He Z. Genomic analysis of Nypa fruticans elucidates its intertidal adaptations and early palm evolution. JOURNAL OF INTEGRATIVE PLANT BIOLOGY 2024;66:824-843. [PMID: 38372488 DOI: 10.1111/jipb.13625] [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: 05/30/2023] [Accepted: 01/28/2024] [Indexed: 02/20/2024]
20
Zhang D, Jakovlić I, Zou H, Liu F, Xiang CY, Gusang Q, Tso S, Xue S, Zhu WJ, Li Z, Wu J, Wang GT. Strong mitonuclear discordance in the phylogeny of Neodermata and evolutionary rates of Polyopisthocotylea. Int J Parasitol 2024;54:213-223. [PMID: 38185351 DOI: 10.1016/j.ijpara.2024.01.001] [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: 08/11/2023] [Revised: 12/03/2023] [Accepted: 01/02/2024] [Indexed: 01/09/2024]
21
Wirthlin ME, Schmid TA, Elie JE, Zhang X, Kowalczyk A, Redlich R, Shvareva VA, Rakuljic A, Ji MB, Bhat NS, Kaplow IM, Schäffer DE, Lawler AJ, Wang AZ, Phan BN, Annaldasula S, Brown AR, Lu T, Lim BK, Azim E, Clark NL, Meyer WK, Pond SLK, Chikina M, Yartsev MM, Pfenning AR, Andrews G, Armstrong JC, Bianchi M, Birren BW, Bredemeyer KR, Breit AM, Christmas MJ, Clawson H, Damas J, Di Palma F, Diekhans M, Dong MX, Eizirik E, Fan K, Fanter C, Foley NM, Forsberg-Nilsson K, Garcia CJ, Gatesy J, Gazal S, Genereux DP, Goodman L, Grimshaw J, Halsey MK, Harris AJ, Hickey G, Hiller M, Hindle AG, Hubley RM, Hughes GM, Johnson J, Juan D, Kaplow IM, Karlsson EK, Keough KC, Kirilenko B, Koepfli KP, Korstian JM, Kowalczyk A, Kozyrev SV, Lawler AJ, Lawless C, Lehmann T, Levesque DL, Lewin HA, Li X, Lind A, Lindblad-Toh K, Mackay-Smith A, Marinescu VD, Marques-Bonet T, Mason VC, Meadows JRS, Meyer WK, Moore JE, Moreira LR, Moreno-Santillan DD, Morrill KM, Muntané G, Murphy WJ, Navarro A, Nweeia M, Ortmann S, Osmanski A, Paten B, Paulat NS, Pfenning AR, Phan BN, Pollard KS, Pratt HE, Ray DA, Reilly SK, Rosen JR, Ruf I, Ryan L, Ryder OA, Sabeti PC, Schäffer DE, Serres A, Shapiro B, Smit AFA, Springer M, Srinivasan C, Steiner C, Storer JM, Sullivan KAM, Sullivan PF, Sundström E, Supple MA, Swofford R, Talbot JE, Teeling E, Turner-Maier J, Valenzuela A, Wagner F, Wallerman O, Wang C, Wang J, Weng Z, Wilder AP, Wirthlin ME, Xue JR, Zhang X. Vocal learning-associated convergent evolution in mammalian proteins and regulatory elements. Science 2024;383:eabn3263. [PMID: 38422184 DOI: 10.1126/science.abn3263] [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: 11/18/2021] [Accepted: 02/20/2024] [Indexed: 03/02/2024]
22
Benito JB, Porter ML, Niemiller ML. Comparative mitogenomic analysis of subterranean and surface amphipods (Crustacea, Amphipoda) with special reference to the family Crangonyctidae. BMC Genomics 2024;25:298. [PMID: 38509489 PMCID: PMC10956265 DOI: 10.1186/s12864-024-10111-w] [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: 06/20/2023] [Accepted: 02/09/2024] [Indexed: 03/22/2024]  Open
23
Chandra S, Abhilash R, Sidharthan A, Raghavan R, Dahanukar N. Complete mitogenome of Lepidopygopsis typus, an evolutionarily-distinct, endangered cyprinid fish from the Western Ghats Biodiversity Hotspot: Phylogenetic relationships and implications for conservation. Gene 2024;898:148098. [PMID: 38128794 DOI: 10.1016/j.gene.2023.148098] [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: 10/29/2023] [Revised: 12/08/2023] [Accepted: 12/18/2023] [Indexed: 12/23/2023]
24
Nunes WVB, Oliveira DS, Dias GDR, Carvalho AB, Caruso ÍP, Biselli JM, Guegen N, Akkouche A, Burlet N, Vieira C, Carareto CMA. A comprehensive evolutionary scenario for the origin and neofunctionalization of the Drosophila speciation gene Odysseus (OdsH). G3 (BETHESDA, MD.) 2024;14:jkad299. [PMID: 38156703 PMCID: PMC10917504 DOI: 10.1093/g3journal/jkad299] [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: 11/22/2023] [Revised: 11/22/2023] [Accepted: 12/20/2023] [Indexed: 01/03/2024]
25
Courcelle M, Salami H, Tounkara K, Lo MM, Ba A, Diop M, Niang M, Sidibe CAK, Sery A, Dakouo M, Kaba L, Sidime Y, Keyra M, Diallo AOS, El Mamy AB, El Arbi AS, Barry Y, Isselmou E, Habiboullah H, Doumbia B, Gueya MB, Awuni J, Odoom T, Ababio PT, TawiahYingar DNY, Coste C, Guendouz S, Kwiatek O, Libeau G, Bataille A. Comparative evolutionary analyses of peste des petits ruminants virus genetic lineages. Virus Evol 2024;10:veae012. [PMID: 38476867 PMCID: PMC10930206 DOI: 10.1093/ve/veae012] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/10/2023] [Revised: 01/16/2024] [Accepted: 03/05/2024] [Indexed: 03/14/2024]  Open
26
Arya M, Ghosh A, Tyagi K, Tyagi I, Bisht SS, Kumar V. Characterization of Complete Mitochondrial Genome of Badri Breed of Bos indicus (Bovidae: Bovinae): Selection Pressure and Comparative Analysis. Biochem Genet 2024:10.1007/s10528-024-10691-y. [PMID: 38407767 DOI: 10.1007/s10528-024-10691-y] [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: 10/09/2023] [Accepted: 01/05/2024] [Indexed: 02/27/2024]
27
Policarpo M, Baldwin MW, Casane D, Salzburger W. Diversity and evolution of the vertebrate chemoreceptor gene repertoire. Nat Commun 2024;15:1421. [PMID: 38360851 PMCID: PMC10869828 DOI: 10.1038/s41467-024-45500-y] [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: 09/22/2023] [Accepted: 01/23/2024] [Indexed: 02/17/2024]  Open
28
Zhao L, Zhou W, He J, Li DZ, Li HT. Positive selection and relaxed purifying selection contribute to rapid evolution of male-biased genes in a dioecious flowering plant. eLife 2024;12:RP89941. [PMID: 38353667 PMCID: PMC10942601 DOI: 10.7554/elife.89941] [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] [Indexed: 02/16/2024]  Open
29
Chouaia B, Dittmer J. A 2000-Year-Old Bacillus stercoris Strain Sheds Light on the Evolution of Cyclic Antimicrobial Lipopeptide Synthesis. Microorganisms 2024;12:338. [PMID: 38399742 PMCID: PMC10893106 DOI: 10.3390/microorganisms12020338] [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: 11/18/2023] [Revised: 01/25/2024] [Accepted: 01/30/2024] [Indexed: 02/25/2024]  Open
30
Cui R, Wu J, Yan K, Luo S, Hu Y, Feng W, Lu B, Wang J. Phased genome assemblies reveal haplotype-specific genetic load in the critically endangered Chinese Bahaba (Teleostei, Sciaenidae). Mol Ecol 2024;33:e17250. [PMID: 38179694 DOI: 10.1111/mec.17250] [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: 06/24/2023] [Revised: 12/06/2023] [Accepted: 12/11/2023] [Indexed: 01/06/2024]
31
Hauser FE, Xiao D, Van Nynatten A, Brochu-De Luca KK, Rajakulendran T, Elbassiouny AE, Sivanesan H, Sivananthan P, Crampton WGR, Lovejoy NR. Ecologically mediated differences in electric organ discharge drive evolution in a sodium channel gene in South American electric fishes. Biol Lett 2024;20:20230480. [PMID: 38412964 PMCID: PMC10898970 DOI: 10.1098/rsbl.2023.0480] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/13/2023] [Accepted: 01/29/2024] [Indexed: 02/29/2024]  Open
32
Estevez-Castro CF, Rodrigues MF, Babarit A, Ferreira FV, de Andrade EG, Marois E, Cogni R, Aguiar ERGR, Marques JT, Olmo RP. Neofunctionalization driven by positive selection led to the retention of the loqs2 gene encoding an Aedes specific dsRNA binding protein. BMC Biol 2024;22:14. [PMID: 38273313 PMCID: PMC10809485 DOI: 10.1186/s12915-024-01821-4] [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: 02/07/2022] [Accepted: 01/10/2024] [Indexed: 01/27/2024]  Open
33
Maurer-Alcalá XX, Cote-L’Heureux A, Kosakovsky Pond SL, Katz LA. Somatic genome architecture and molecular evolution are decoupled in "young" linage-specific gene families in ciliates. PLoS One 2024;19:e0291688. [PMID: 38271450 PMCID: PMC10810533 DOI: 10.1371/journal.pone.0291688] [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: 03/11/2023] [Accepted: 09/02/2023] [Indexed: 01/27/2024]  Open
34
Iverson ENK, Criswell A, Havird JC. Stronger evidence for relaxed selection than adaptive evolution in high-elevation animal mtDNA. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2024:2024.01.20.576402. [PMID: 38328137 PMCID: PMC10849488 DOI: 10.1101/2024.01.20.576402] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 02/09/2024]
35
Yépez Y, Marcano-Ruiz M, Bortolini MC. Adaptive strategies of aquatic mammals: Exploring the role of the HIF pathway and hypoxia tolerance. Genet Mol Biol 2024;46:e20230140. [PMID: 38252060 PMCID: PMC10802827 DOI: 10.1590/1678-4685-gmb-2023-0140] [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: 05/08/2023] [Accepted: 12/06/2023] [Indexed: 01/23/2024]  Open
36
Wierz JC, Gimmel ML, Huthmacher S, Engl T, Kaltenpoth M. Evolutionary history of tyrosine-supplementing endosymbionts in pollen-feeding beetles. THE ISME JOURNAL 2024;18:wrae080. [PMID: 38861456 PMCID: PMC11191362 DOI: 10.1093/ismejo/wrae080] [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: 02/02/2024] [Revised: 04/24/2024] [Accepted: 04/30/2024] [Indexed: 06/13/2024]
37
Pucker B, Walker‐Hale N, Dzurlic J, Yim WC, Cushman JC, Crum A, Yang Y, Brockington SF. Multiple mechanisms explain loss of anthocyanins from betalain-pigmented Caryophyllales, including repeated wholesale loss of a key anthocyanidin synthesis enzyme. THE NEW PHYTOLOGIST 2024;241:471-489. [PMID: 37897060 PMCID: PMC10952170 DOI: 10.1111/nph.19341] [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: 09/11/2022] [Accepted: 09/23/2023] [Indexed: 10/29/2023]
38
Feldmeyer B, Bornberg-Bauer E, Dohmen E, Fouks B, Heckenhauer J, Huylmans AK, Jones ARC, Stolle E, Harrison MC. Comparative Evolutionary Genomics in Insects. Methods Mol Biol 2024;2802:473-514. [PMID: 38819569 DOI: 10.1007/978-1-0716-3838-5_16] [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] [Indexed: 06/01/2024]
39
Liu Q, Cai YD, Ma L, Liu H, Linghu T, Guo S, Wei S, Song F, Tian L, Cai W, Li H. Relaxed purifying selection pressure drives accelerated and dynamic gene rearrangements in thrips (Insecta: Thysanoptera) mitochondrial genomes. Int J Biol Macromol 2023;253:126742. [PMID: 37689283 DOI: 10.1016/j.ijbiomac.2023.126742] [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: 05/12/2023] [Revised: 08/06/2023] [Accepted: 08/26/2023] [Indexed: 09/11/2023]
40
Wang K, Wang J, Liang B, Chang J, Zhu Y, Chen J, Agnarsson I, Li D, Peng Y, Liu J. Eyeless cave-dwelling Leptonetela spiders still rely on light. SCIENCE ADVANCES 2023;9:eadj0348. [PMID: 38117895 PMCID: PMC10732526 DOI: 10.1126/sciadv.adj0348] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/03/2023] [Accepted: 11/17/2023] [Indexed: 12/22/2023]
41
Fu CN, Wicke S, Zhu AD, Li DZ, Gao LM. Distinctive plastome evolution in carnivorous angiosperms. BMC PLANT BIOLOGY 2023;23:660. [PMID: 38124058 PMCID: PMC10731798 DOI: 10.1186/s12870-023-04682-1] [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: 07/14/2023] [Accepted: 12/11/2023] [Indexed: 12/23/2023]
42
Levis NA, Ragsdale EJ. A histone demethylase links the loss of plasticity to nongenetic inheritance and morphological change. Nat Commun 2023;14:8439. [PMID: 38114491 PMCID: PMC10730525 DOI: 10.1038/s41467-023-44306-8] [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: 02/13/2023] [Accepted: 12/07/2023] [Indexed: 12/21/2023]  Open
43
Wainwright JB, Schofield C, Conway M, Phillips D, Martin-Silverstone E, Brodrick EA, Cicconardi F, How MJ, Roberts NW, Montgomery SH. Multiple axes of visual system diversity in Ithomiini, an ecologically diverse tribe of mimetic butterflies. J Exp Biol 2023;226:jeb246423. [PMID: 37921078 PMCID: PMC10714147 DOI: 10.1242/jeb.246423] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/18/2023] [Accepted: 10/31/2023] [Indexed: 11/04/2023]
44
Drabeck DH, Wiese J, Gilbertson E, Arroyave J, Arcila D, Alter SE, Borowsky R, Hendrickson D, Stiassny M, McGaugh SE. Gene loss and relaxed selection of plaat1 in vertebrates adapted to low-light environments. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2023:2023.12.12.571336. [PMID: 38168154 PMCID: PMC10760033 DOI: 10.1101/2023.12.12.571336] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/05/2024]
45
Ludington AJ, Hammond JM, Breen J, Deveson IW, Sanders KL. New chromosome-scale genomes provide insights into marine adaptations of sea snakes (Hydrophis: Elapidae). BMC Biol 2023;21:284. [PMID: 38066641 PMCID: PMC10709897 DOI: 10.1186/s12915-023-01772-2] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/02/2023] [Accepted: 11/20/2023] [Indexed: 12/18/2023]  Open
46
Zhao Y, Zheng Z, Zhang Z, Xu Y, Hillpot E, Lin YS, Zakusilo FT, Lu JY, Ablaeva J, Biashad SA, Miller RA, Nevo E, Seluanov A, Gorbunova V. Evolution of high-molecular-mass hyaluronic acid is associated with subterranean lifestyle. Nat Commun 2023;14:8054. [PMID: 38052795 PMCID: PMC10698142 DOI: 10.1038/s41467-023-43623-2] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/03/2022] [Accepted: 11/15/2023] [Indexed: 12/07/2023]  Open
47
Ramos E, Selleghin-Veiga G, Magpali L, Daros B, Silva F, Picorelli A, Freitas L, Nery MF. Molecular Footprints on Osmoregulation-Related Genes Associated with Freshwater Colonization by Cetaceans and Sirenians. J Mol Evol 2023;91:865-881. [PMID: 38010516 DOI: 10.1007/s00239-023-10141-0] [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: 02/04/2023] [Accepted: 10/29/2023] [Indexed: 11/29/2023]
48
Bryłka K, Pinseel E, Roberts WR, Ruck EC, Conley DJ, Alverson AJ. Gene Duplication, Shifting Selection, and Dosage Balance of Silicon Transporter Proteins in Marine and Freshwater Diatoms. Genome Biol Evol 2023;15:evad212. [PMID: 37996067 PMCID: PMC10700740 DOI: 10.1093/gbe/evad212] [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: 07/06/2023] [Revised: 09/15/2023] [Accepted: 11/17/2023] [Indexed: 11/25/2023]  Open
49
Mulhair PO, Crowley L, Boyes DH, Lewis OT, Holland PWH. Opsin Gene Duplication in Lepidoptera: Retrotransposition, Sex Linkage, and Gene Expression. Mol Biol Evol 2023;40:msad241. [PMID: 37935057 PMCID: PMC10642689 DOI: 10.1093/molbev/msad241] [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: 08/16/2023] [Revised: 10/20/2023] [Accepted: 10/26/2023] [Indexed: 11/09/2023]  Open
50
Desvignes T, Bista I, Herrera K, Landes A, Postlethwait JH. Cold-Driven Hemoglobin Evolution in Antarctic Notothenioid Fishes Prior to Hemoglobin Gene Loss in White-Blooded Icefishes. Mol Biol Evol 2023;40:msad236. [PMID: 37879119 PMCID: PMC10651078 DOI: 10.1093/molbev/msad236] [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: 05/25/2023] [Revised: 09/08/2023] [Accepted: 10/18/2023] [Indexed: 10/27/2023]  Open
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