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Number Cited by Other Article(s)
1
Shafir A, Halabi K, Baumer E, Mayrose I. ChromEvol v.3: modeling rate heterogeneity in chromosome number evolution. THE NEW PHYTOLOGIST 2025;245:1787-1800. [PMID: 39676573 DOI: 10.1111/nph.20339] [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: 06/23/2024] [Accepted: 11/22/2024] [Indexed: 12/17/2024]
2
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]
3
Yan H, Hu Z, Thomas GWC, Edwards SV, Sackton TB, Liu JS. PhyloAcc-GT: A Bayesian Method for Inferring Patterns of Substitution Rate Shifts on Targeted Lineages Accounting for Gene Tree Discordance. Mol Biol Evol 2023;40:msad195. [PMID: 37665177 PMCID: PMC10540510 DOI: 10.1093/molbev/msad195] [Citation(s) in RCA: 8] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/23/2022] [Revised: 08/15/2023] [Accepted: 09/01/2023] [Indexed: 09/05/2023]  Open
4
Pereira AG, Kohlsdorf T. Repeated evolution of similar phenotypes: Integrating comparative methods with developmental pathways. Genet Mol Biol 2023;46:e20220384. [PMID: 37486083 PMCID: PMC10364090 DOI: 10.1590/1678-4685-gmb-2022-0384] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/28/2022] [Accepted: 05/24/2023] [Indexed: 07/25/2023]  Open
5
Pereira AG, Grizante MB, Kohlsdorf T. What snakes and caecilians have in common? Molecular interaction units and the independent origins of similar morphotypes in Tetrapoda. Proc Biol Sci 2022;289:20220841. [PMID: 35975445 PMCID: PMC9382212 DOI: 10.1098/rspb.2022.0841] [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: 05/01/2022] [Accepted: 07/25/2022] [Indexed: 12/14/2022]  Open
6
de Oliveira Martins L, Bloomfield S, Stoakes E, Grant AJ, Page AJ, Mather AE. Tatajuba: exploring the distribution of homopolymer tracts. NAR Genom Bioinform 2022;4:lqac003. [PMID: 35118377 PMCID: PMC8808543 DOI: 10.1093/nargab/lqac003] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/02/2021] [Revised: 11/18/2021] [Accepted: 01/05/2022] [Indexed: 11/14/2022]  Open
7
Jones CT, Youssef N, Susko E, Bielawski JP. A Phenotype-Genotype Codon Model for Detecting Adaptive Evolution. Syst Biol 2021;69:722-738. [PMID: 31730199 DOI: 10.1093/sysbio/syz075] [Citation(s) in RCA: 9] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/07/2019] [Revised: 11/09/2019] [Accepted: 11/11/2019] [Indexed: 01/03/2023]  Open
8
May MR, Moore BR. A Bayesian Approach for Inferring the Impact of a Discrete Character on Rates of Continuous-Character Evolution in the Presence of Background-Rate Variation. Syst Biol 2020;69:530-544. [PMID: 31665487 PMCID: PMC7608729 DOI: 10.1093/sysbio/syz069] [Citation(s) in RCA: 24] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/13/2019] [Accepted: 10/21/2019] [Indexed: 11/14/2022]  Open
9
Halabi K, Karin EL, Guéguen L, Mayrose I. A Codon Model for Associating Phenotypic Traits with Altered Selective Patterns of Sequence Evolution. Syst Biol 2020;70:608-622. [PMID: 33252676 DOI: 10.1093/sysbio/syaa087] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/01/2020] [Revised: 11/12/2020] [Accepted: 11/13/2020] [Indexed: 01/10/2023]  Open
10
Mayrose I, Lysak MA. The Evolution of Chromosome Numbers: Mechanistic Models and Experimental Approaches. Genome Biol Evol 2020;13:5923296. [PMID: 33566095 PMCID: PMC7875004 DOI: 10.1093/gbe/evaa220] [Citation(s) in RCA: 37] [Impact Index Per Article: 7.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 10/12/2020] [Indexed: 12/16/2022]  Open
11
The plastid NAD(P)H dehydrogenase-like complex: structure, function and evolutionary dynamics. Biochem J 2020;476:2743-2756. [PMID: 31654059 DOI: 10.1042/bcj20190365] [Citation(s) in RCA: 20] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/17/2019] [Revised: 08/27/2019] [Accepted: 09/02/2019] [Indexed: 11/17/2022]
12
Guindon S. Rates and Rocks: Strengths and Weaknesses of Molecular Dating Methods. Front Genet 2020;11:526. [PMID: 32536940 PMCID: PMC7267027 DOI: 10.3389/fgene.2020.00526] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/18/2019] [Accepted: 04/30/2020] [Indexed: 12/19/2022]  Open
13
Smith SD, Pennell MW, Dunn CW, Edwards SV. Phylogenetics is the New Genetics (for Most of Biodiversity). Trends Ecol Evol 2020;35:415-425. [DOI: 10.1016/j.tree.2020.01.005] [Citation(s) in RCA: 65] [Impact Index Per Article: 13.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/14/2019] [Revised: 01/15/2020] [Accepted: 01/20/2020] [Indexed: 12/15/2022]
14
Yusuf L, Heatley MC, Palmer JPG, Barton HJ, Cooney CR, Gossmann TI. Noncoding regions underpin avian bill shape diversification at macroevolutionary scales. Genome Res 2020;30:553-565. [PMID: 32269134 PMCID: PMC7197477 DOI: 10.1101/gr.255752.119] [Citation(s) in RCA: 25] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/09/2019] [Accepted: 03/17/2020] [Indexed: 12/18/2022]
15
Goldberg EE, Foo J. Memory in Trait Macroevolution. Am Nat 2020;195:300-314. [DOI: 10.1086/705992] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/03/2022]
16
Barrett CF, Sinn BT, Kennedy AH. Unprecedented Parallel Photosynthetic Losses in a Heterotrophic Orchid Genus. Mol Biol Evol 2019;36:1884-1901. [PMID: 31058965 PMCID: PMC6736286 DOI: 10.1093/molbev/msz111] [Citation(s) in RCA: 36] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/12/2022]  Open
17
Lamichhaney S, Card DC, Grayson P, Tonini JFR, Bravo GA, Näpflin K, Termignoni-Garcia F, Torres C, Burbrink F, Clarke JA, Sackton TB, Edwards SV. Integrating natural history collections and comparative genomics to study the genetic architecture of convergent evolution. Philos Trans R Soc Lond B Biol Sci 2019;374:20180248. [PMID: 31154982 PMCID: PMC6560268 DOI: 10.1098/rstb.2018.0248] [Citation(s) in RCA: 31] [Impact Index Per Article: 5.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 02/25/2019] [Indexed: 12/20/2022]  Open
18
Ashkenazy H, Levy Karin E, Mertens Z, Cartwright RA, Pupko T. SpartaABC: a web server to simulate sequences with indel parameters inferred using an approximate Bayesian computation algorithm. Nucleic Acids Res 2019;45:W453-W457. [PMID: 28460062 PMCID: PMC5570005 DOI: 10.1093/nar/gkx322] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/06/2017] [Accepted: 04/15/2017] [Indexed: 11/22/2022]  Open
19
Hu Z, Sackton TB, Edwards SV, Liu JS. Bayesian Detection of Convergent Rate Changes of Conserved Noncoding Elements on Phylogenetic Trees. Mol Biol Evol 2019;36:1086-1100. [PMID: 30851112 PMCID: PMC6501877 DOI: 10.1093/molbev/msz049] [Citation(s) in RCA: 39] [Impact Index Per Article: 6.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/19/2022]  Open
20
Blaz J, Barrera-Redondo J, Vázquez-Rosas-Landa M, Canedo-Téxon A, Aguirre von Wobeser E, Carrillo D, Stouthamer R, Eskalen A, Villafán E, Alonso-Sánchez A, Lamelas A, Ibarra-Juarez LA, Pérez-Torres CA, Ibarra-Laclette E. Genomic Signals of Adaptation towards Mutualism and Sociality in Two Ambrosia Beetle Complexes. Life (Basel) 2018;9:E2. [PMID: 30583535 PMCID: PMC6463014 DOI: 10.3390/life9010002] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/14/2018] [Revised: 12/08/2018] [Accepted: 12/20/2018] [Indexed: 01/03/2023]  Open
21
Watson-Lazowski A, Papanicolaou A, Sharwood R, Ghannoum O. Investigating the NAD-ME biochemical pathway within C4 grasses using transcript and amino acid variation in C4 photosynthetic genes. PHOTOSYNTHESIS RESEARCH 2018;138:233-248. [PMID: 30078073 DOI: 10.1007/s11120-018-0569-x] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/25/2018] [Accepted: 07/28/2018] [Indexed: 05/18/2023]
22
Tahir D, Glémin S, Lascoux M, Kaj I. Modeling a trait-dependent diversification process coupled with molecular evolution on a random species tree. J Theor Biol 2018;461:189-203. [PMID: 30340056 DOI: 10.1016/j.jtbi.2018.10.032] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/24/2018] [Revised: 10/10/2018] [Accepted: 10/12/2018] [Indexed: 12/23/2022]
23
Sironi M, Forni D, Clerici M, Cagliani R. Genetic conflicts with Plasmodium parasites and functional constraints shape the evolution of erythrocyte cytoskeletal proteins. Sci Rep 2018;8:14682. [PMID: 30279439 PMCID: PMC6168477 DOI: 10.1038/s41598-018-33049-y] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/14/2018] [Accepted: 09/19/2018] [Indexed: 11/19/2022]  Open
24
Lasky JR, Forester BR, Reimherr M. Coherent synthesis of genomic associations with phenotypes and home environments. Mol Ecol Resour 2017;18:91-106. [DOI: 10.1111/1755-0998.12714] [Citation(s) in RCA: 30] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/15/2016] [Revised: 08/10/2017] [Accepted: 08/25/2017] [Indexed: 01/22/2023]
25
Levy Karin E, Ashkenazy H, Wicke S, Pupko T, Mayrose I. TraitRateProp: a web server for the detection of trait-dependent evolutionary rate shifts in sequence sites. Nucleic Acids Res 2017;45:W260-W264. [PMID: 28453644 PMCID: PMC5570260 DOI: 10.1093/nar/gkx288] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/28/2017] [Revised: 04/02/2017] [Accepted: 04/26/2017] [Indexed: 11/23/2022]  Open
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