Baillon H. Histoire des Plantes, vol. 2. Paris: Librairie Hachette; 1870.
Google Scholar
Kostermans AJGH. Lauraceae. Reinwardtia. 1957;4:193–256.
Google Scholar
van der Werff H, Richter HG. Toward an improved classification of Lauraceae. Ann Mo Bot Gard. 1996;83:409–18.
Article
Google Scholar
Gottlieb OR. Chemosystematics of the lauraceae. Phytochemistry. 1972;11(5):1537–70.
Article
CAS
Google Scholar
Hutchinson J. The genera of flowering plants (Dicotyledonae), vol. 1. Oxford: Clarendon Press; 1964.
Google Scholar
Rohwer JG. Lauraceae. In: Kubitzki K, Rohwer JG, Bittrich V, editors. Flowering plants · Dicotyledons. The families and genera of vascular plants, vol. 2. Berlin Heidelberg: Springer-Verlag; 1993. p. 366–90.
Chapter
Google Scholar
Li J, Conran JG, Christophel DC, Li Z-M, Li L, Li H-W. Phylogenetic relationships of the Litsea complex and core Laureae (Lauraceae) using ITS and ETS sequences and morphology. Ann Mo Bot Gard. 2008;95(4):580–600.
Article
Google Scholar
van der Merwe M, Crayn DM, Ford AJ, Weston PH, Rossetto M. Evolution of Australian Cryptocarya (Lauraceae) based on nuclear and plastid phylogenetic trees: evidence of recent landscape-level disjunctions. Aust Syst Bot. 2016;29(2):157–66.
Article
Google Scholar
Tian Y, Zhou J, Zhang Y, Wang S, Wang Y, Liu H, et al. Research Progress in plant molecular systematics of Lauraceae. Biology. 2021;10(5):391.
Article
CAS
PubMed
PubMed Central
Google Scholar
Rohwer JG. Toward a phylogenetic classification of the Lauraceae: evidence from matK sequences. Syst Bot. 2000;25(1):60–71.
Article
Google Scholar
Chanderbali AS, van der Werff H, Renner SS. Phylogeny and historical biogeography of Lauraceae: evidence from the chloroplast and nuclear genomes. Ann Mo Bot Gard. 2001;88(1):104–34.
Article
Google Scholar
Huang J-F, Li L, van der Werff H, Li H-W, Rohwer JG, Crayn DM, et al. Origins and evolution of cinnamon and camphor: a phylogenetic and historical biogeographical analysis of the Cinnamomum group (Lauraceae). Mol Phylogenet Evol. 2016;96:33–44.
Article
CAS
PubMed
Google Scholar
Penagos Zuluaga JC, van der Werff H, Park B, Eaton DAR, Comita LS, Queenborough SA, et al. Resolved phylogenetic relationships in the Ocotea complex (Supraocotea) facilitate phylogenetic classification and studies of character evolution. Am J Bot. 2021;108(4):664–79.
Article
PubMed
Google Scholar
Trofimov D, Cadar D, Schmidt-Chanasit J, Rodrigues de Moraes PL, Rohwer JG. A comparative analysis of complete chloroplast genomes of seven Ocotea species (Lauraceae) confirms low sequence divergence within the Ocotea complex. Sci Rep. 2022;12(1):1120.
Article
CAS
PubMed
PubMed Central
Google Scholar
Song Y, Yu WB, Tan YH, Jin JJ, Wang B, Yang JB, et al. Plastid phylogenomics improve phylogenetic resolution in the Lauraceae. J Syst Evol. 2020;58(4):423–39.
Article
Google Scholar
Rieseberg LH, Soltis D. Phylogenetic consequences of cytoplasmic gene flow in plants. Evol Trend Plant. 1991;5:65–84.
Google Scholar
Hansen AK, Escobar LK, Gilbert LE, Jansen RK. Paternal, maternal, and biparental inheritance of the chloroplast genome in Passiflora (Passifloraceae): implications for phylogenetic studies. Am J Bot. 2007;94(1):42–6.
Article
CAS
PubMed
Google Scholar
Zhang J-Q, Meng S-Y, Allen GA, Wen J, Rao G-Y. Rapid radiation and dispersal out of the Qinghai-Tibetan plateau of an alpine plant lineage Rhodiola (Crassulaceae). Mol Phylogenet Evol. 2014;77:147–58.
Article
PubMed
Google Scholar
Friesen N, German DA, Hurka H, Herden T, Oyuntsetseg B, Neuffer B. Dated phylogenies and historical biogeography of Dontostemon and Clausia (Brassicaceae) mirror the palaeogeographical history of the Eurasian steppe. J Biogeogr. 2016;43(4):738–49.
Article
Google Scholar
Brandley MC, Wang Y, Guo X, Montes de Oca AN, Fería-Ortíz M, Hikida T, et al. Accommodating heterogenous rates of evolution in molecular divergence dating methods: an example using intercontinental dispersal of Plestiodon (Eumeces) lizards. Syst Biol. 2011;60(1):3–15.
Article
CAS
PubMed
Google Scholar
Gitzendanner MA, Soltis PS, Yi T-S, Li D-Z, Soltis DE. Plastome phylogenetics: 30 years of inferences into plant evolution. In: Chaw S-M, Jansen RK, editors. Advances in botanical ResearchPlant diversity, vol. 85. London: Academic Press; 2018. p. 293–313.
Google Scholar
Doyle JJ, Doyle JL. A rapid DNA isolation procedure for small quantities of fresh leaf tissue. Phytochem Bull. 1987;19:11–5.
Google Scholar
Bolger AM, Lohse M, Usadel B. Trimmomatic: a flexible trimmer for Illumina sequence data. Bioinformatics. 2014;30(15):2114–20.
Article
CAS
PubMed
PubMed Central
Google Scholar
Andrews S. FastQC: a quality control tool for high throughput sequence data. 2010. http://www.bioinformatics.babraham.ac.uk/projects/fastqc. Accessed 15 Oct 2021.
Google Scholar
Dierckxsens N, Mardulyn P, Smits G. NOVOPlasty: de novo assembly of organelle genomes from whole genome data. Nucleic Acids Res. 2016;45(4):e18–e.
PubMed Central
Google Scholar
Jin J-J, Yu W-B, Yang J-B, Song Y, dePamphilis CW, Yi T-S, et al. GetOrganelle: a fast and versatile toolkit for accurate de novo assembly of organelle genomes. Genome Biol. 2020;21(1):241.
Article
PubMed
PubMed Central
Google Scholar
Li H, Durbin R. Fast and accurate long-read alignment with Burrows–Wheeler transform. Bioinformatics. 2010;26(5):589–95.
Article
PubMed
PubMed Central
CAS
Google Scholar
Li H, Handsaker B, Wysoker A, Fennell T, Ruan J, Homer N, et al. The sequence alignment/map format and SAMtools. Bioinformatics. 2009;25(16):2078–9.
Article
PubMed
PubMed Central
CAS
Google Scholar
Kearse M, Moir R, Wilson A, Stones-Havas S, Cheung M, Sturrock S, et al. Geneious basic: an integrated and extendable desktop software platform for the organization and analysis of sequence data. Bioinformatics. 2012;28(12):1647–9.
Article
PubMed
PubMed Central
Google Scholar
Tillich M, Lehwark P, Pellizzer T, Ulbricht-Jones ES, Fischer A, Bock R, et al. GeSeq - versatile and accurate annotation of organelle genomes. Nucleic Acids Res. 2017;45(W1):W6–W11.
Article
CAS
PubMed
PubMed Central
Google Scholar
Lohse M, Drechsel O, Kahlau S, Bock R. OrganellarGenomeDRAW—a suite of tools for generating physical maps of plastid and mitochondrial genomes and visualizing expression data sets. Nucleic Acids Res. 2013;41(W1):W575–W81.
Article
PubMed
PubMed Central
Google Scholar
Darling AC, Mau B, Blattner FR, Perna NT. Mauve: multiple alignment of conserved genomic sequence with rearrangements. Genome Res. 2004;14(7):1394–403.
Article
CAS
PubMed
PubMed Central
Google Scholar
Amiryousefi A, Hyvönen J, Poczai P. IRscope: an online program to visualize the junction sites of chloroplast genomes. Bioinformatics. 2018;34(17):3030–1.
Article
CAS
PubMed
Google Scholar
Frazer KA, Pachter L, Poliakov A, Rubin EM, Dubchak I. VISTA: computational tools for comparative genomics. Nucleic Acids Res. 2004;32(suppl_2):W273–W9.
Article
CAS
PubMed
PubMed Central
Google Scholar
Katoh K, Standley DM. MAFFT multiple sequence alignment software version 7: improvements in performance and usability. Mol Biol Evol. 2013;30(4):772–80.
Article
CAS
PubMed
PubMed Central
Google Scholar
Librado P, Rozas J. DnaSP v5: a software for comprehensive analysis of DNA polymorphism data. Bioinformatics. 2009;25(11):1451–2.
Article
CAS
PubMed
Google Scholar
Wickham H. ggplot2: elegant graphics for data analysis. New York: Springer-Verlag; 2016.
Book
Google Scholar
R Core Team. R: The R Project for Statistical Computing. 2021. https://www.r-project.org. Accessed 15 Dec 2021.
Kurtz S, Choudhuri JV, Ohlebusch E, Schleiermacher C, Stoye J, Giegerich R. REPuter: the manifold applications of repeat analysis on a genomic scale. Nucleic Acids Res. 2001;29(22):4633–42.
Article
CAS
PubMed
PubMed Central
Google Scholar
Beier S, Thiel T, Münch T, Scholz U, Mascher M. MISA-web: a wFrontiers in plant Scienceeb server for microsatellite prediction. Bioinformatics. 2017;33(16):2583–5.
Article
CAS
PubMed
PubMed Central
Google Scholar
Benson G. Tandem repeats finder: a program to analyze DNA sequences. Nucleic Acids Res. 1999;27(2):573–80.
Article
CAS
PubMed
PubMed Central
Google Scholar
Duvall MR, Burke SV, Clark DC. Plastome phylogenomics of Poaceae: alternate topologies depend on alignment gaps. Bot J Linn Soc. 2020;192(1):9–20.
Article
Google Scholar
Orton LM, Barbera P, Nissenbaum MP, Peterson PM, Quintanar A, Soreng RJ, et al. A 313 plastome phylogenomic analysis of Pooideae: exploring relationships among the largest subfamily of grasses. Mol Phylogenet Evol. 2021;159:107110.
Article
PubMed
Google Scholar
Steenwyk JL, Buida TJ III, Li Y, Shen X-X, Rokas A. ClipKIT: a multiple sequence alignment trimming software for accurate phylogenomic inference. PLoS Biol. 2020;18(12):e3001007.
Article
CAS
PubMed
PubMed Central
Google Scholar
Borowiec ML. AMAS: a fast tool for alignment manipulation and computing of summary statistics. PeerJ. 2016;4:e1660.
Article
PubMed
PubMed Central
Google Scholar
Stamatakis A. RAxML version 8: a tool for phylogenetic analysis and post-analysis of large phylogenies. Bioinformatics. 2014;30(9):1312–3.
Article
CAS
PubMed
PubMed Central
Google Scholar
Yang Z. PAML 4: phylogenetic analysis by maximum likelihood. Mol Biol Evol. 2007;24(8):1586–91.
Article
CAS
PubMed
Google Scholar
Xiao T-W, Xu Y, Jin L, Liu T-J, Yan H-F, Ge X-J. Conflicting phylogenetic signals in plastomes of the tribe Laureae (Lauraceae). PeerJ. 2020;8:e10155.
Article
PubMed
PubMed Central
Google Scholar
Kumar S, Stecher G, Li M, Knyaz C, Tamura K. MEGA X: molecular evolutionary genetics analysis across computing platforms. Mol Biol Evol. 2018;35(6):1547–9.
Article
CAS
PubMed
PubMed Central
Google Scholar
Yang Z, Nielsen R. Codon-substitution models for detecting molecular adaptation at individual sites along specific lineages. Mol Biol Evol. 2002;19(6):908–17.
Article
CAS
PubMed
Google Scholar
Bouckaert R, Heled J, Kühnert D, Vaughan T, Wu C-H, Xie D, et al. BEAST 2: a software platform for bayesian evolutionary analysis. PLoS Comp Biol. 2014;10(4):e1003537.
Article
CAS
Google Scholar
Darriba D, Posada D, Kozlov AM, Stamatakis A, Morel B, Flouri T, et al. ModelTest-NG: a new and scalable tool for the selection of DNA and protein evolutionary models. Mol Biol Evol. 2020;37(1):291–4.
Article
CAS
PubMed
Google Scholar
Friis EM, Eklund H, Pedersen KR, Crane PR. Virginianthus calycanthoides gen. Et sp. nov.-a Calycanthaceous flower from the Potomac group (early cretaceous) of eastern North America. Int J Plant Sci. 1994;155(6):772–85.
Article
Google Scholar
Li H, Liu B, Davis CC, Yang Y. Plastome phylogenomics, systematics, and divergence time estimation of the Beilschmiedia group (Lauraceae). Mol Phylogenet Evol. 2020;151:106901.
Article
PubMed
Google Scholar
Kondraskov P, Schütz N, Schüßler C, de Sequeira MM, Guerra AS, Caujapé-Castells J, et al. Biogeography of Mediterranean hotspot biodiversity: re-evaluating the 'Tertiary Relict' hypothesis of Macaronesian Laurel forests. PLoS One. 2015;10(7):e0132091.
Article
PubMed
PubMed Central
CAS
Google Scholar
Eklund H. Lauraceous flowers from the late cretaceous of North Carolina, U.S.A. Bot J Linn Soc. 2000;132(4):397–428.
Article
Google Scholar
Atkinson BA, Stockey RA, Rothwell GW, Mindell RA, Bolton MJ. Lauraceous flowers from the Eocene of Vancouver Island: Tinaflora beardiae gen. Et sp. nov. (Lauraceae). Int J Plant Sci. 2015;176(6):567–85.
Article
Google Scholar
Tang B, Han M, Xu Q, Jin J. Leaf cuticle microstructure of Machilus maomingensis sp. nov. (Lauraceae) from the Eocene of the Maoming basin, South China. Acta Geol Sin - Engl. 2016;90(5):1561–71.
Article
Google Scholar
Rambaut A, Drummond AJ, Xie D, Baele G, Suchard MA. Posterior summarization in bayesian phylogenetics using tracer 1.7. Syst Biol. 2018;67(5):901–4.
Article
CAS
PubMed
PubMed Central
Google Scholar
Chen C, Zheng Y, Liu S, Zhong Y, Wu Y, Li J, et al. The complete chloroplast genome of Cinnamomum camphora and its comparison with related Lauraceae species. PeerJ. 2017;5:e3820.
Article
PubMed
PubMed Central
CAS
Google Scholar
Song Y, Yu WB, Tan Y, Liu B, Yao X, Jin J, et al. Evolutionary comparisons of the chloroplast genome in Lauraceae and insights into loss events in the Magnoliids. Genome Biol Evol. 2017;9(9):2354–64.
Article
CAS
PubMed
PubMed Central
Google Scholar
Mower JP, Guo W, Partha R, Fan W, Levsen N, Wolff K, et al. Plastomes from tribe Plantagineae (Plantaginaceae) reveal infrageneric structural synapormorphies and localized hypermutation for Plantago and functional loss of ndh genes from Littorella. Mol Phylogenet Evol. 2021;162:107217.
Article
PubMed
Google Scholar
Weng M-L, Ruhlman TA, Jansen RK. Expansion of inverted repeat does not decrease substitution rates in Pelargonium plastid genomes. New Phytol. 2017;214(2):842–51.
Article
CAS
PubMed
Google Scholar
Wei N, Pérez-Escobar OA, Musili PM, Huang W-C, Yang J-B, Hu A-Q, et al. Plastome evolution in the Hyperdiverse genus Euphorbia (Euphorbiaceae) using Phylogenomic and comparative analyses: large-scale expansion and contraction of the inverted repeat region. Front Plant Sci. 2021;12:712064.
Article
PubMed
PubMed Central
Google Scholar
Lee C, Choi IS, Cardoso D, de Lima HC, de Queiroz LP, Wojciechowski MF, et al. The chicken or the egg? Plastome evolution and an independent loss of the inverted repeat in papilionoid legumes. Plant J. 2021;107(3):861–75.
Article
CAS
PubMed
Google Scholar
Goulding SE, Wolfe KH, Olmstead RG, Morden CW. Ebb and flow of the chloroplast inverted repeat. Mol Gen Genet MGG. 1996;252(1):195–206.
Article
CAS
PubMed
Google Scholar
Wang R-J, Cheng C-L, Chang C-C, Wu C-L, Su T-M, Chaw S-M. Dynamics and evolution of the inverted repeat-large single copy junctions in the chloroplast genomes of monocots. BMC Evol Biol. 2008;8(1):36.
Article
CAS
PubMed
PubMed Central
Google Scholar
Zhang L, Wang S, Su C, Harris A, Zhao L, Su N, et al. Comparative chloroplast genomics and phylogenetic analysis of Zygophyllum (Zygophyllaceae) of China. Front Plant Sci. 2021;12:723622.
Article
PubMed
PubMed Central
Google Scholar
Cao Q, Gao Q, Ma X, Zhang F, Xing R, Chi X, et al. Plastome structure, phylogenomics and evolution of plastid genes in Swertia (Gentianaceae) in the Qing-Tibetan plateau. BMC Plant Biol. 2022;22(1):195.
Article
CAS
PubMed
PubMed Central
Google Scholar
Weng M-L, Blazier JC, Govindu M, Jansen RK. Reconstruction of the ancestral plastid genome in Geraniaceae reveals a correlation between genome rearrangements, repeats, and nucleotide substitution rates. Mol Biol Evol. 2014;31(3):645–59.
Article
CAS
PubMed
Google Scholar
Yang Q, Fu G-F, Wu Z-Q, Li L, Zhao J-L, Li Q-J. Chloroplast genome evolution in four Montane Zingiberaceae taxa in China. Front Plant Sci. 2022;12:774482.
Article
PubMed
PubMed Central
Google Scholar
Gui L, Jiang S, Xie D, Yu L, Huang Y, Zhang Z, et al. Analysis of complete chloroplast genomes of Curcuma and the contribution to phylogeny and adaptive evolution. Gene. 2020;732:144355.
Article
CAS
PubMed
Google Scholar
Piot A, Hackel J, Christin P-A, Besnard G. One-third of the plastid genes evolved under positive selection in PACMAD grasses. Planta. 2018;247(1):255–66.
Article
CAS
PubMed
Google Scholar
Drescher A, Ruf S, Calsa T Jr, Carrer H, Bock R. The two largest chloroplast genome-encoded open reading frames of higher plants are essential genes. Plant J. 2000;22(2):97–104.
Article
CAS
PubMed
Google Scholar
Kikuchi S, Asakura Y, Imai M, Nakahira Y, Kotani Y, Hashiguchi Y, et al. A Ycf2-FtsHi Heteromeric AAA-ATPase complex is required for chloroplast protein import. Plant Cell. 2018;30(11):2677–703.
Article
CAS
PubMed
PubMed Central
Google Scholar
Kapralov MV, Filatov DA. Widespread positive selection in the photosynthetic Rubisco enzyme. BMC Evol Biol. 2007;7(1):73.
Article
PubMed
PubMed Central
CAS
Google Scholar
Kapralov MV, Filatov DA. Molecular adaptation during adaptive radiation in the Hawaiian endemic genus Schiedea. PLoS One. 2006;1(1):e8.
Article
PubMed
PubMed Central
CAS
Google Scholar
CBOL Plant Working Group, Hollingsworth Peter M, Forrest Laura L, Spouge John L, Hajibabaei M, Ratnasingham S, et al. A DNA barcode for land plants. Proc Natl Acad Sci U S A. 2009;106(31):12794–7.
Article
PubMed Central
Google Scholar
Kress WJ. Plant DNA barcodes: applications today and in the future. J Syst Evol. 2017;55(4):291–307.
Article
Google Scholar
Lu L-M, Mao L-F, Yang T, Ye J-F, Liu B, Li H-L, et al. Evolutionary history of the angiosperm flora of China. Nature. 2018;554(7691):234–8.
Article
CAS
PubMed
Google Scholar
Kress WJ, García-Robledo C, Uriarte M, Erickson DL. DNA barcodes for ecology, evolution, and conservation. Trends Ecol Evol. 2015;30(1):25–35.
Article
PubMed
Google Scholar
Li X-Q, Xiang X-G, Zhang Q, Jabbour F, Ortiz RC, Erst AS, et al. Immigration dynamics of tropical and subtropical Southeast Asian limestone karst floras. Proc Royal Soc B. 1966;2022(289):20211308.
Google Scholar
Starr JR, Naczi RFC, Chouinard BN. Plant DNA barcodes and species resolution in sedges (Carex, Cyperaceae). Mol Ecol Resour. 2009;9(s1):151–63.
Article
CAS
PubMed
Google Scholar
Dong W, Xu C, Li C, Sun J, Zuo Y, Shi S, et al. ycf1, the most promising plastid DNA barcode of land plants. Sci Rep. 2015;5(1):8348.
Article
CAS
PubMed
PubMed Central
Google Scholar
Liu C, Chen H-H, Tang L-Z, Khine PK, Han L-H, Song Y, et al. Plastid genome evolution of a monophyletic group in the subtribe lauriineae (Laureae, Lauraceae). Plant Divers. 2021. https://doi.org/10.1016/j.pld.2021.11.009.
Whitfield JB, Lockhart PJ. Deciphering ancient rapid radiations. Trends Ecol Evol. 2007;22(5):258–65.
Article
PubMed
Google Scholar
Suh A, Smeds L, Ellegren H. The dynamics of incomplete lineage sorting across the ancient adaptive radiation of Neoavian birds. PLoS Biol. 2015;13(8):e1002224.
Article
PubMed
PubMed Central
CAS
Google Scholar
Yu Y, Than C, Degnan JH, Nakhleh L. Coalescent histories on phylogenetic networks and detection of hybridization despite incomplete lineage sorting. Syst Biol. 2011;60(2):138–49.
Article
CAS
PubMed
PubMed Central
Google Scholar
Rose JP, Toledo CAP, Lemmon EM, Lemmon AR, Sytsma KJ. Out of sight, out of mind: widespread nuclear and plastid-nuclear discordance in the flowering plant genus Polemonium (Polemoniaceae) suggests widespread historical gene flow despite limited nuclear signal. Syst Biol. 2021;70(1):162–80.
Article
CAS
PubMed
Google Scholar
Zhou B-F, Yuan S, Crowl AA, Liang Y-Y, Shi Y, Chen X-Y, et al. Phylogenomic analyses highlight innovation and introgression in the continental radiations of Fagaceae across the northern hemisphere. Nat Commun. 2022;13(1):1320.
Article
CAS
PubMed
PubMed Central
Google Scholar
Trofimov D, Rohwer JG. Towards a phylogenetic classification of the Ocotea complex (Lauraceae): an analysis with emphasis on the Old World taxa and description of the new genus Kuloa. Bot J Linn Soc. 2020;192(3):510–35.
Article
Google Scholar
Tiffney BH. Perspectives on the origin of the floristic similarity between eastern Asia and eastern North America. J Arnold Arboretum. 1985;66:73–94.
Article
Google Scholar
Wolfe JA. Some aspects of plant geography of the northern hemisphere during the late cretaceous and tertiary. Ann Mo Bot Gard. 1975;62:264–79.
Article
Google Scholar