Nuclear phylogenomics of angiosperms and insights into their relationships and evolution

Abstract

Angiosperms (flowering plants) are by far the most diverse land plant group with over 300,000 species. The sudden appearance of diverse angiosperms in the fossil record was referred to by Darwin as the “abominable mystery,” hence contributing to the heightened interest in angiosperm evolution. Angiosperms display wide ranges of morphological, physiological, and ecological characters, some of which have probably influenced their species richness. The evolutionary analyses of these characteristics help to address questions of angiosperm diversification and require well resolved phylogeny. Following the great successes of phylogenetic analyses using plastid sequences, dozens to thousands of nuclear genes from next-generation sequencing have been used in angiosperm phylogenomic analyses, providing well resolved phylogenies and new insights into the evolution of angiosperms. In this review we focus on recent nuclear phylogenomic analyses of large angiosperm clades, orders, families, and subdivisions of some families and provide a summarized Nuclear Phylogenetic Tree of Angiosperm Families. The newly established nuclear phylogenetic relationships are highlighted and compared with previous phylogenetic results. The sequenced genomes of Amborella, Nymphaea, Chloranthus, Ceratophyllum, and species of monocots, Magnoliids, and basal eudicots, have facilitated the phylogenomics of relationships among five major angiosperms clades. All but one of the 64 angiosperm orders were included in nuclear phylogenomics with well resolved relationships except the placements of several orders. Most families have been included with robust and highly supported placements, especially for relationships within several large and important orders and families. Additionally, we examine the divergence time estimation and biogeographic analyses of angiosperm on the basis of the nuclear phylogenomic frameworks and discuss the differences compared with previous analyses. Furthermore, we discuss the implications of nuclear phylogenomic analyses on ancestral reconstruction of morphological, physiological, and ecological characters of angiosperm groups, limitations of current nuclear phylogenomic studies, and the taxa that require future attention.

Keywords

angiosperms / evolution / flowering plants / nuclear gene / phylogenomics / phylogeny

References

[1] Abair, A., Hughes, C.E., and Bailey, C.D. (2019). The evolutionary history of Leucaena: Recent research, new genomic resources and future directions. Trop. Grasslands-Forrajes Trop. 7: 65-73.

[2] Ai, B., Gao, Y., Zhang, X., Tao, J., Kang, M., and Huang, H. (2015). Comparative transcriptome resources of eleven Primulina species, a group of “stone plants” from a biodiversity hot spot. Mol. Ecol. Resour. 15: 619-632.

[3] Ali, M.A., Rahman, M.O., Lee, J., Hemaid, F. Al, Kambhar, S.V., Elangbam, M., and Gurung, A.B. (2020). Dissecting molecular evolutionary relationship of Krameriaceae inferred from phylotranscriptomic analysis. Bangladesh J. Plant Taxon. 27: 427-433.

[4] Álvarez, I., Costa, A., and Feliner, G.N. (2008). Selecting single-copy nuclear genes for plant phylogenetics: A preliminary analysis for the Senecioneae (Asteraceae). J. Mol. Evol. 66: 276-291.

[5] Amarasinghe, P., Pham, P., Stone, R.D., and Cellinese, N. (2021). Discordance in a South African Memecylon clade (Melastomataceae): Evidence for reticulate evolution. Int. J. Plant Sci. 182: 682-694.

[6] Ananda, G., Norton, S., Blomstedt, C., Furtado, A., Møller, B., Gleadow, R., and Henry, R. (2021). Phylogenetic relationships in the Sorghum genus based on sequencing of the chloroplast and nuclear genes. Plant Genome 14: e20123.

[7] Antonelli, A., Clarkson, J.J., Kainulainen, K., Maurin, O., Brewer, G.E., Davis, A.P., Epitawalage, N., Goyder, D.J., Livshultz, T., Persson, C., et al. (2021). Settling a family feud: A high-level phylogenomic framework for the Gentianales based on 353 nuclear genes and partial plastomes. Am. J. Bot. 108: 1143-1165.

[8] Bagley, J.C., Uribe-Convers, S., Carlsen, M.M., and Muchhala, N. (2020). Utility of targeted sequence capture for phylogenomics in rapid, recent angiosperm radiations: Neotropical Burmeistera bellflowers as a case study. Mol. Phylogenet. Evol. 152: 106769.

[9] Baldwin, B.G., and Markos, S. (1998). Phylogenetic utility of the External Transcribed Spacer (ETS) of 18S-26S rDNA: Congruence of ETS and ITS trees of Calycadenia (Compositae). Mol. Phylogenet. Evol. 10: 449-463.

[10] Baldwin, B.G., Sanderson, M.J., Porter, J.M., Wojciechowski, M.F., Campbell, C.S., and Donoghue, M.J. (1995). The ITS region of nuclear ribosomal DNA: A valuable source of evidence on angiosperm phylogeny. Ann. Missouri Bot. Gard. 82: 247.

[11] Benton, M.L., Abraham, A., LaBella, A.L., Abbot, P., Rokas, A., and Capra, J.A. (2021). The influence of evolutionary history on human health and disease. Nat. Rev. Genet. 22: 269-283.

[12] Berendse, F., and Scheffer, M. (2009). The angiosperm radiation revisited, an ecological explanation for Darwin's “abominable mystery”. Ecol. Lett. 12: 865.

[13] Boulter, D. (1973). Amino acid sequences of cytochrome c and plastocyanins in phylogenetic studies of higher plants. Syst. Zool. 22: 549-553.

[14] Boulter, D., Peacock, D., Guise, A., Gleaves, J.T., and Estabrook, G. (1979). Relationships between the partial amino acid sequences of plastocyanin from members of ten families of flowering plants. Phytochemistry 18: 603-608.

[15] Brassac, J., and Blattner, F.R. (2015). Species-level phylogeny and polyploid relationships in Hordeum (Poaceae) inferred by next-generation sequencing and in silico cloning of multiple nuclear loci. Syst. Biol. 64: 792-808.

[16] Bremer, B., Bremer, K., Chase, M.W., Fay, M.F., Reveal, J.L., Bailey, L.H., Soltis, D.E., Soltis, P.S., Stevens, P.F., Anderberg, A.A., et al. (2009). An update of the Angiosperm Phylogeny Group classification for the orders and families of flowering plants: APG III. Bot. J. Linn. Soc. 161: 105-121.

[17] Bremer, B., Bremer, K., Chase, M.W., Reveal, J.L., Soltis, D.E., Soltis, P.S., Stevens, P.F., Anderberg, A.A., Fay, M.F., Goldblatt, P., et al. (2003). An update of the Angiosperm Phylogeny Group classification for the orders and families of flowering plants: APG II. Bot. J. Linn. Soc. 141: 399-436.

[18] Bremer, K., Chase, M., Stevens, P., Anderberg, A., Backlund, A., Bremer, B., Briggs, B.G., Endress, P.K., Fay, M., Goldblatt, P., et al. (1998). An ordinal classification for the families of flowering plants. Ann. Missouri Bot. Gard. 85: 531.

[19] Brock, J.R., Dönmez, A.A., Beilstein, M.A., and Olsen, K.M. (2018). Phylogenetics of Camelina Crantz. (Brassicaceae) and insights on the origin of gold-of-pleasure (Camelina sativa). Mol. Phylogenet. Evol. 127: 834-842.

[20] Buggs, R.J.A. (2017). The deepening of Darwin's abominable mystery. Nat. Ecol. Evol. 1: 1-2.

[21] Buggs, R.J.A. (2021). The origin of Darwin's “abominable mystery”. Am. J. Bot. 108: 22-36.

[22] Cai, L., and Ma, H. (2016). Using nuclear genes to reconstruct angiosperm phylogeny at the species level: A case study with Brassicaceae species. J. Syst. Evol. 54: 438-452.

[23] Cai, L., Xi, Z., Lemmon, E.M., Lemmon, A.R., Mast, A., Buddenhagen, C.E., Liu, L., and Davis, C.C. (2021). The perfect storm: Gene tree estimation error, incomplete lineage sorting, and ancient gene llow explain the most recalcitrant ancient angiosperm clade, Malpighiales. Syst. Biol. 70: 491-507.

[24] Carlsen, M.M., Fér, T., Schmickl, R., Leong-Škorničková, J., Newman, M., and Kress, W.J. (2018). Resolving the rapid plant radiation of early diverging lineages in the tropical Zingiberales: Pushing the limits of genomic data. Mol. Phylogenet. Evol. 128: 55-68.

[25] Carter, K.A., Liston, A., Bassil, N.V., Alice, L.A., Bushakra, J.M., Sutherland, B.L., Mockler, T.C., Bryant, D.W., and Hummer, K.E. (2019). Target capture sequencing unravels Rubus evolution. Front. Plant Sci. 10: 1615.

[26] Cavender-Bares, J., González-Rodríguez, A., Eaton, D.A.R., Hipp, A.A.L., Beulke, A., and Manos, P.S. (2015). Phylogeny and biogeography of the American live oaks (Quercus subsection Virentes): A genomic and population genetics approach. Mol. Ecol. 24: 3668-3687.

[27] Chanderbali, A.S., Jin, L., Xu, Q., Zhang, Y., Zhang, J., Jian, S., Carroll, E., Sankoff, D., Albert, V.A., Howarth, D.G., et al. (2022). Buxus and Tetracentron genomes help resolve eudicot genome history. Nat. Commun. 13: 1-10.

[28] Chaowasku, T. (2020). Toward a phylogenetic reclassification of the subfamily Ambavioideae (Annonaceae): Establishment of a new subfamily and a new tribe. Acta Bot. Brasilica 34: 522-529.

[29] Chase, M., Fay, M., Devey, D., Maurin, O., Rønsted, N., Davies, J., Pillon, Y., Peterson, G., Tamura, M., Asmussen, C., et al. (2006). Multigene analyses of monocot relationships. Aliso 22: 63-75.

[30] Chase, M.W., Christenhusz, M.J.M., Fay, M.F., Byng, J.W., Judd, W.S., Soltis, D.E., Mabberley, D.J., Sennikov, A.N., Soltis, P.S., Stevens, P.F., et al. (2016). An update of the Angiosperm Phylogeny Group classification for the orders and families of flowering plants: APG IV. Bot. J. Linn. Soc. 181: 1-20.

[31] Chase, M.W., Soltis, D.E., Olmstead, R.G., Morgan, D., Les, D.H., Mishler, B.D., Duvall, M.R., Price, R.A., Hills, H.G., Qiu, Y.-L., et al. (1993). Phylogenetics of seed plants: An analysis of nucleotide sequences from the plastid gene rbcL. Ann. Missouri Bot. Gard 80: 528.

[32] Chaw, S.M., Liu, Y.C., Wu, Y.W., Wang, H.Y., Lin, C.Y.I., Wu, C.S., Ke, H.M., Chang, L.Y., Hsu, C.Y., Yang, H.T., et al. (2019). Stout camphor tree genome fills gaps in understanding of flowering plant genome evolution. Nat. Plants 51: 63-73.

[33] Chen, C., Ruhfel, B.R., Li, J., Wang, Z., Zhang, L.ushui, Zhang, L.ei, Mao, X., Wang, J., He, D., Luo, Y., et al. (2023a). Phylotranscriptomics of Swertiinae (Gentianaceae) reveals that key floral traits are not phylogenetically correlated. J. Integr. Plant Biol. 65: 1490-1504.

[34] Chen, C.L., Zhang, L., Li, J.L., Mao, X.X., Zhang, L.S., Hu, Q.J., Liu, J.Q., and Xi, Z.X. (2021). Phylotranscriptomics reveals extensive gene duplication in the subtribe Gentianinae (Gentianaceae). J. Syst. Evol. 59: 1198-1208.

[35] Chen, J., Lidén, M., Huang, X., Zhang, L., Zhang, X., Kuang, T., Landis, J.B., Wang, D., Deng, T., and Sun, H. (2023b). An updated classification for the hyper-diverse genus Corydalis (Papaveraceae: Fumarioideae) based on phylogenomic and morphological evidence. J. Integr. Plant Biol. 65: 2138-2156.

[36] Chen, L.Y., Lu, B., Morales-Briones, D.F., Moody, M.L., Liu, F., Hu, G.W., Huang, C.H., Chen, J.M., and Wang, Q.F. (2022). Phylogenomic analyses of Alismatales shed light into adaptations to aquatic environments. Mol. Biol. Evol. 39: 79.

[37] Cheng, L., Li, M., Han, Q., Qiao, Z., Hao, Y., Balbuena, T.S., and Zhao, Y. (2022). Phylogenomics resolves the phylogeny of Theaceae by using low-copy and multi-copy nuclear gene makers and uncovers a fast radiation event contributing to tea plants diversity. Biology 11: 1007.

[38] Choi, I.S., Cardoso, D., de Queiroz, L.P., de Lima, H.C., Lee, C., Ruhlman, T.A., Jansen, R.K., and Wojciechowski, M.F. (2022). Highly resolved Papilionoid legume phylogeny based on plastid phylogenomics. Front. Plant Sci. 13: 823190.

[39] Christe, C., Boluda, C.G., Koubínová, D., Gautier, L., and Naciri, Y. (2021). New genetic markers for Sapotaceae phylogenomics: More than 600 nuclear genes applicable from family to population levels. Mol. Phylogenet. Evol. 160: 107123.

[40] Clarkson, J.J., Zuntini, A.R., Maurin, O., Downie, S.R., Plunkett, G.M., Nicolas, A.N., Smith, J.F., Feist, M.A.E., Gutierrez, K., Malakasi, P., et al. (2021). A higher-level nuclear phylogenomic study of the carrot family (Apiaceae). Am. J. Bot. 108: 1252-1269.

[41] Comer, J.R., Zomlefer, W.B., Barrett, C.F., Stevenson, D.W., Heyduk, K., and Leebens-Mack, J.H. (2016). Nuclear phylogenomics of the palm subfamily Arecoideae (Arecaceae). Mol. Phylogenet. Evol. 97: 32-42.

[42] Couvreur, T.L.P., Helmstetter, A.J., Koenen, E.J.M., Bethune, K., Brandão, R.D., Little, S.A., Sauquet, H., and Erkens, R.H.J. (2019). Phylogenomics of the major tropical plant family Annonaceae using targeted enrichment of nuclear genes. Front. Plant Sci. 9: 1941.

[43] Coyne, J.A., Elwyn, S., Kim, S.Y., and Llopart, A. (2004). Genetic studies of two sister species in the Drosophila melanogaster subgroup, D. yakuba and D. santomea. Genet. Res. 84: 11-26.

[44] dePamphilis, C.W., Palmer, J.D., Rounsley, S., Sankoff, D., Schuster, S.C., Ammiraju, J.S.S., Barbazuk, W.B., Chamala, S., Chanderbali, A.S., Determann, R., et al. (2013). The Amborella genome and the evolution of flowering plants. Science 342: 1241089.

[45] Dobzhansky, T. (1973). Nothing in biology makes sense except in the light of evolution. Am. Biol. Teach. 35: 125-129.

[46] Dong, S.S., Wang, Y.L., Xia, N.H., Liu, Y., Liu, M., Lian, L., Li, N., Li, L.F., Lang, X.A., Gong, Y.Q., et al. (2022a). Plastid and nuclear phylogenomic incongruences and biogeographic implications of Magnolia s.l. (Magnoliaceae). J. Syst. Evol. 60: 1-15.

[47] Dong, W.P., Sun, J.H., Liu, Y.L., Xu, C., Wang, Y.H., Suo, Z.L., Zhou, S.L., Zhang, Z.X., and Wen, J. (2022b). Phylogenomic relationships and species identification of the olive genus Olea (Oleaceae). J. Syst. Evol. 60: 1263-1280.

[48] Duan, L., Han, L.N., Liu, B., Bin , Leostrin, A., Harris, A.J., Wang, L., Arslan, E., Ertuğrul, K., Knyazev, M., et al. (2023). Species delimitation of the liquorice tribe (Leguminosae: Glycyrrhizeae) based on phylogenomic and machine learning analyses. J. Syst. Evol. 61: 22-41.

[49] Edger, P.P., Heidel-Fischer, H.M., Bekaert, M., Rota, J., Glöckner, G., Platts, A.E., Heckel, D.G., Der, J.P., Wafula, E.K., Tang, M., et al. (2015). The butterfly plant arms-race escalated by gene and genome duplications. Proc. Natl. Acad. Sci. U.S.A. 112: 8362-8366.

[50] Endress, P.K., and Doyle, J.A. (2009). Reconstructing the ancestral angiosperm flower and its initial specializations. Am. J. Bot. 96: 22-66.

[51] Eserman, L.A., Thomas, S.K., Coffey, E.E.D., and Leebens-Mack, J.H. (2021). Target sequence capture in orchids: Developing a kit to sequence hundreds of single-copy loci. Appl. Plant Sci. 9: e11416.

[52] Fitz-Gibbon, S., Hipp, A.L., Pham, K.K., Manos, P.S., and Sork, V.L. (2017). Phylogenomic inferences from reference-mapped and de novo assembled short-read sequence data using RADseq sequencing of California white oaks (Quercus section Quercus). Genome 60: 743-755.

[53] Folk, R.A., Mandel, J.R., and Freudenstein, J.V. (2015). A Protocol for targeted enrichment of intron-containing sequence markers for recent radiations: A phylogenomic example from Heuchera (Saxifragaceae). Appl. Plant Sci. 3: 1500039.

[54] Fonseca, L.H.M., Carlsen, M.M., Fine, P.V.A., and Lohmann, L.G. (2023). A nuclear target sequence capture probe set for phylogeny reconstruction of the charismatic plant family Bignoniaceae. Front. Genet. 13: 1085692.

[55] Fu, C.N., Mo, Z.Q., Yang, J.B., Ge, X.J., Li, D.Z., Xiang, Q.Y., (Jenny ), and Gao, L.M. (2019). Plastid phylogenomics and biogeographic analysis support a trans-Tethyan origin and rapid early radiation of Cornales in the Mid-Cretaceous. Mol. Phylogenet. Evol. 140: 106601.

[56] Futuyma, D.J. (2017). Evolutionary biology today and the call for an extended synthesis. Interface Focus 7: 20160145.

[57] Gagnon, E., Hilgenhof, R., Orejuela, A., McDonnell, A., Sablok, G., Aubriot, X., Giacomin, L., Gouvêa, Y., Bragionis, T., Stehmann, J.R., et al. (2022). Phylogenomic discordance suggests polytomies along the backbone of the large genus Solanum. Am. J. Bot. 109: 580-601.

[58] García, N., Folk, R.A., Meerow, A.W., Chamala, S., Gitzendanner, M.A., Oliveira, R.S., de Soltis, D.E., and Soltis, P.S. (2017). Deep reticulation and incomplete lineage sorting obscure the diploid phylogeny of rain-lilies and allies (Amaryllidaceae tribe Hippeastreae). Mol. Phylogenet. Evol. 111: 231-247.

[59] Gitzendanner, M.A., Soltis, P.S., Wong, G.K.-S., Ruhfel, B.R., and Soltis, D.E. (2018). Plastid phylogenomic analysis of green plants: A billion years of evolutionary history. Am. J. Bot. 105: 291-301.

[60] Givnish, T.J., Spalink, D., Ames, M., Lyon, S.P., Hunter, S.J., Zuluaga, A., Doucette, A., Caro, G.G., McDaniel, J., Clements, M.A., et al. (2016a). Orchid historical biogeography, diversification, Antarctica and the paradox of orchid dispersal. J. Biogeogr. 43: 1905-1916.

[61] Givnish, T.J., Spalink, D., Ames, M., Lyon, S.P., Hunter, S.J., Zuluaga, A., Iles, W.J.D., Clements, M.A., Arroyo, M.T.K., Leebens-Mack, J., et al. (2015). Orchid phylogenomics and multiple drivers of their extraordinary diversification. Proc. R. Soc. B Biol. Sci. 282: 20151553.

[62] Givnish, T.J., Zuluaga, A., Marques, I., Lam, V.K.Y., Gomez, M.S., Iles, W.J.D., Ames, M., Spalink, D., Moeller, J.R., Briggs, B.G., et al. (2016b). Phylogenomics and historical biogeography of the monocot order Liliales: Out of Australia and through Antarctica. Cladistics 32: 581-605.

[63] Givnish, T.J., Zuluaga, A., Spalink, D., Soto Gomez, M., Lam, V.K.Y., Saarela, J.M., Sass, C., Iles, W.J.D., de Sousa, D.J.L., Leebens-Mack, J., et al. (2018). Monocot plastid phylogenomics, timeline, net rates of species diversification, the power of multi-gene analyses, and a functional model for the origin of monocots. Am. J. Bot. 105: 1888-1910.

[64] Godden, G.T., Kinser, T.J., Soltis, P.S., Soltis, D.E., and Chaw, S.M. (2019). Phylotranscriptomic analyses reveal asymmetrical gene duplication dynamics and signatures of ancient polyploidy in mints. Genome Biol. Evol. 11: 3393-3408.

[65] Gontier, N. (2011). Depicting the tree of life: The philosophical and historical roots of evolutionary tree diagrams. Evol. Educ. Outreach 4: 515-538.

[66] Govindarajulu, R., Parks, M., Tennessen, J.A., Liston, A., and Ashman, T.L. (2015). Comparison of nuclear, plastid, and mitochondrial phylogenies and the origin of wild octoploid strawberry species. Am. J. Bot. 102: 544-554.

[67] Graham, S.W., and Olmstead, R.G. (2000). Utility of 17 chloroplast genes for inferring the phylogeny of the basal angiosperms. Am. J. Bot. 87: 1712-1730.

[68] Griesmann, M., Chang, Y., Liu, X., Song, Y., Haberer, G., Crook, M.B., Billault-Penneteau, B., Lauressergues, D., Keller, J., Imanishi, L., et al. (2018). Phylogenomics reveals multiple losses of nitrogen-fixing root nodule symbiosis. Science 361: eaat1743.

[69] Guo, C., Guo, Z.-H., and Li, D.-Z. (2019). Phylogenomic analyses reveal intractable evolutionary history of a temperate bamboo genus (Poaceae: Bambusoideae). Plant Divers 41: 213-219.

[70] Guo, C., Luo, Y., Gao, L.M., Yi, T.S., Li, H.T., Yang, J.B., and Li, D.Z. (2023). Phylogenomics and the flowering plant tree of life. J. Integr. Plant Biol. 65: 299-323.

[71] Guo, J., Xu, W., Hu, Y., Huang, J., Zhao, Y., Zhang, L., Huang, C.H., and Ma, H. (2020). Phylotranscriptomics in Cucurbitaceae reveal multiple whole-genome duplications and key morphological and molecular innovations. Mol. Plant 13: 1117-1133.

[72] Guo, X., Fang, D., Sahu, S.K., Yang, S., Guang, X., Folk, R., Smith, S.A., Chanderbali, A.S., Chen, S., Liu, M., et al. (2021). Chloranthus genome provides insights into the early diversification of angiosperms. Nat. Commun. 12: 6930.

[73] Hao, D.C., Li, P., Xiao, P.G., and He, C.N. (2021). Dissection of full-length transcriptome and metabolome of Dichocarpum (Ranunculaceae): Implications in evolution of specialized metabolism of Ranunculales medicinal plants. PeerJ 9: e12428.

[74] Hazra, A., Das, S.ubhanwita, Bhattacharya, S., Sur, S., Sengupta, C., and Das, S.auren (2021). Phylogenetic inference of Ericales based on plastid genomes and implication of cp-SSRs. BioTechnol. 102: 277.

[75] He, J., Lyu, R., Luo, Y., Xiao, J., Xie, L., Wen, J., Li, W., Pei, L., and Cheng, J. (2022). A phylotranscriptome study using silica gel-dried leaf tissues produces an updated robust phylogeny of Ranunculaceae. Mol. Phylogenet. Evol. 174: 107545.

[76] Hendriks, K.P., Kiefer, C., Al-Shehbaz, I.A., Bailey, C.D., Huysduynen, A.H., van Nikolov, L.A., Nauheimer, L., Zuntini, A.R., German, D.A., Franzke, A., et al. (2022). Global phylogeny of the Brassicaceae provides important insights into gene discordance. Curr. Biol. 33: 4052-4068.

[77] Henriquez, C.L., Arias, T., Pires, J.C., Croat, T.B., and Schaal, B.A. (2014). Phylogenomics of the plant family Araceae. Mol. Phylogenet. Evol. 75: 91-102.

[78] Herrando-Moraira, S., Calleja, J.A., Galbany-Casals, M., Garcia-Jacas, N., Liu, J.-Q., López-Alvarado, J., López-Pujol, J., Mandel, J.R., Massó, S., Montes-Moreno, N., et al. (2019). Nuclear and plastid DNA phylogeny of tribe Cardueae (Compositae) with Hyb-Seq data: A new subtribal classification and a temporal diversification framework. Mol. Phylogenet. Evol. 137: 313-332.

[79] Heyduk, K., Trapnell, D.W., Barrett, C.F., and Leebens-Mack, J. (2016). Phylogenomic analyses of species relationships in the genus Sabal (Arecaceae) using targeted sequence capture. Biol. J. Linn. Soc. 117: 106-120.

[80] Hipp, A.L., Eaton, D.A.R., Cavender-Bares, J., Fitzek, E., Nipper, R., and Manos, P.S. (2014). A framework phylogeny of the American oak clade based on sequenced RAD data. PLoS ONE 9: e93975.

[81] Hodel, R.G.J., Zimmer, E., and Wen, J. (2021). A phylogenomic approach resolves the backbone of Prunus (Rosaceae) and identifies signals of hybridization and allopolyploidy. Mol. Phylogenet. Evol. 160: 107118.

[82] Hodel, R.G.J., Zimmer, E.A., Liu, B.-B., and Wen, J. (2022). Synthesis of nuclear and chloroplast data combined with network analyses supports the polyploid origin of the apple tribe and the hybrid origin of the Maleae—Gillenieae clade. Front. Plant Sci. 12: 3321.

[83] Hu, H., Sun, P., Yang, Y., Ma, J., and Liu, J. (2023). Genome-scale angiosperm phylogenies based on nuclear, plastome, and mitochondrial datasets. J. Integr. Plant Biol. 65: 1479-1489.

[84] Huang, C.H., Sun, R., Hu, Y., Zeng, L., Zhang, N., Cai, L., Zhang, Q., Koch, M.A., Al-Shehbaz, I., Edger, P.P., et al. (2016b). Resolution of Brassicaceae phylogeny using nuclear genes uncovers nested radiations and supports convergent morphological evolution. Mol. Biol. Evol. 33: 394-412.

[85] Huang, C.-H., Zhang, C., Liu, M., Hu, Y., Gao, T., Qi, J., and Ma, H. (2016a). Multiple polyploidization events across Asteraceae with two nested events in the early history revealed by nuclear phylogenomics. Mol. Biol. Evol. 33: 2820-2835.

[86] Huang, J., Xu, W., Zhai, J., Hu, Y., Guo, J., Zhang, C., Zhao, Y., Zhang, L., Martine, C., Ma, H., et al. (2023). Nuclear phylogeny and insights into whole-genome duplications and reproductive development of Solanaceae plants. Plant Commun. 4: 100595.

[87] Huang, W., Zhang, L., Columbus, J.T., Hu, Y., Zhao, Y., Tang, L., Guo, Z., Chen, W., McKain, M., Bartlett, M., et al. (2022). A well-supported nuclear phylogeny of Poaceae and implications for the evolution of C4 photosynthesis. Mol. Plant 15: 755-777.

[88] Ishizaki, K. (2017). Evolution of land plants: Insights from molecular studies on basal lineages. Biosci. Biotechnol. Biochem. 81: 73-80.

[89] Julca, I., Vargas, P., and Gabaldón, T. (2023). Phylogenomics of the Olea europaea complex using 15 whole genomes supports recurrent genetic admixture together with differentiation into seven subspecies. BMC Biol. 21: 85.

[90] Kadam, S.K., Tamboli, A.S., Mane, R.N., Yadav, S.R., Choo, Y.S., Burgos-Hernández, M., and Pak, J.H. (2023). Revised molecular phylogeny, global biogeography, and diversification of palms subfamily Coryphoideae (Arecaceae) based on low copy nuclear and plastid regions. J. Plant Res. 136: 159-177.

[91] Kamneva, O.K., Syring, J., Liston, A., and Rosenberg, N.A. (2017). Evaluating allopolyploid origins in strawberries (Fragaria) using haplotypes generated from target capture sequencing. BMC Evol. Biol. 17: 1-19.

[92] Kapli, P., Yang, Z., and Telford, M.J. (2020). Phylogenetic tree building in the genomic age. Nat. Rev. Genet. 21: 428-444.

[93] Kates, H.R., Soltis, P.S., and Soltis, D.E. (2017). Evolutionary and domestication history of Cucurbita (pumpkin and squash) species inferred from 44 nuclear loci. Mol. Phylogenet. Evol. 111: 98-109.

[94] Khoshravesh, R., Stata, M., Adachi, S., Sage, T.L., and Sage, R.F. (2020). Evolutionary convergence of C4 photosynthesis: A case study in the Nyctaginaceae. Front. Plant Sci. 11: 1660.

[95] Koenen, E.J.M., Kidner, C., De Souza, É.R., Simon, M.F., Iganci, J.R., Nicholls, J.A., Brown, G.K., De Queiroz, L.P., Luckow, M., Lewis, G.P., et al. (2020a). Hybrid capture of 964 nuclear genes resolves evolutionary relationships in the mimosoid legumes and reveals the polytomous origins of a large pantropical radiation. Am. J. Bot. 107: 1710-1735.

[96] Koenen, E.J.M., Ojeda, D.I., Steeves, R., Migliore, J., Bakker, F.T., Wieringa, J.J., Kidner, C., Hardy, O.J., Pennington, R.T., Bruneau, A., et al. (2020b). Large-scale genomic sequence data resolve the deepest divergences in the legume phylogeny and support a near-simultaneous evolutionary origin of all six subfamilies. New Phytol. 225: 1355-1369.

[97] Lagomarsino, L.P., Frankel, L., Uribe-Convers, S., Antonelli, A., and Muchhala, N. (2022). Increased resolution in the face of conflict: Phylogenomics of the Neotropical bellflowers (Campanulaceae: Lobelioideae), a rapid plant radiation. Ann. Bot. 129: 723-736.

[98] Larson, D.A., Walker, J.F., Vargas, O.M., and Smith, S.A. (2020). A consensus phylogenomic approach highlights paleopolyploid and rapid radiation in the history of Ericales. Am. J. Bot. 107: 773-789.

[99] Leaché, A.D., Banbury, B.L., Felsenstein, J., De Oca, A.N.M., and Stamatakis, A. (2015). Short tree, long tree, right tree, wrong tree: New acquisition bias corrections for inferring SNP phylogenies. Syst. Biol. 64: 1032-1047.

[100] Leaché, A.D., and Oaks, J.R. (2017). The utility of single nucleotide polymorphism (SNP) data in phylogenetics. Annu. Rev. Ecol. Evol. Syst. 48: 69-84.

[101] Lee, A.K., Gilman, I.S., Srivastav, M., Lerner, A.D., Donoghue, M.J., Clement, W.L., Lee, A.K., Gilman, I.S., Srivastav, M., Lerner, A.D., et al. (2021). Reconstructing Dipsacales phylogeny using Angiosperms353: Issues and insights. Am. J. Bot. 108: 1122-1142.

[102] Leebens-Mack, J.H., Barker, M.S., Carpenter, E.J., Deyholos, M.K., Gitzendanner, M.A., Graham, S.W., Grosse, I., Li, Z., Melkonian, M., Mirarab, S., et al. (2019). One thousand plant transcriptomes and the phylogenomics of green plants. Nature 574: 679-685.

[103] Lee-Yaw, J.A., Grassa, C.J., Joly, S., Andrew, R.L., and Rieseberg, L.H. (2019). An evaluation of alternative explanations for widespread cytonuclear discordance in annual sunflowers (Helianthus). New Phytol. 221: 515-526.

[104] Léveillé-Bourret, É., Starr, J.R., Ford, B.A., Moriarty Lemmon, E., and Lemmon, A.R. (2018). Resolving rapid radiations within angiosperm families using anchored phylogenomics. Syst. Biol. 67: 94-112.

[105] Li, H., Huang, C.-H., and Ma, H. (2019a). Whole-genome duplications in pear and apple. In The Pear Genome, S.S. Korban, ed (Cham: Springer), pp. 279-299.

[106] Li, H.T., Luo, Y., Gan, L., Ma, P.F., Gao, L.M., Yang, J.B., Cai, J., Gitzendanner, M.A., Fritsch, P.W., Zhang, T., et al. (2021). Plastid phylogenomic insights into relationships of all flowering plant families. BMC Biol. 19: 1-13.

[107] Li, H.T., Yi, T.S., Gao, L.M., Ma, P.F., Zhang, T., Yang, J.B., Gitzendanner, M.A., Fritsch, P.W., Cai, J., Luo, Y., et al. (2019b). Origin of angiosperms and the puzzle of the Jurassic gap. Nat. Plants 5: 461-470.

[108] Li, Y.X., Li, Z.H., Schuitman, A., Chase, M.W., Li, J.W., Huang, W.C., Hidayat, A., Wu, S.S., and Jin, X.H. (2019c). Phylogenomics of Orchidaceae based on plastid and mitochondrial genomes. Mol. Phylogenet. Evol. 139: 106540.

[109] Li, Z., and Barker, M.S. (2020). Inferring putative ancient whole-genome duplications in the 1,000 plants (1KP) initiative: Access to gene family phylogenies and age distributions. Gigascience 9: giaa004.

[110] Li, Z., De La Torre, A.R., Sterck, L., Cánovas, F.M., Avila, C., Merino, I., Cabezas, J.A., Cervera, M.T., Ingvarsson, P.K., and Van De Peer, Y. (2017). Single-copy genes as molecularmarkers for phylogenomic studies in seed plants. Genome Biol. Evol. 9: 1130-1147.

[111] Lin, G.N., Zhang, C., and Xu, D. (2011). Polytomy identification in microbial phylogenetic reconstruction. BMC Syst. Biol. 5: 1-11.

[112] Liston, A., Weitemier, K.A., Letelier, L., Podani, J., Zong, Y., Liu, L., and Dickinson, T.A. (2021). Phylogeny of Crataegus (Rosaceae) based on 257 nuclear loci and chloroplast genomes: Evaluating the impact of hybridization. PeerJ 9: e12418.

[113] Liu, B., Tan, Y.-H., Liu, S., Olmstead, R.G., Min, D.-Z., Chen, Z.-D., Joshee, N., Vaidya, B.N., Chung, R.C.K., and Li, B. (2020b). Phylogenetic relationships of Cyrtandromoea and Wightia revisited: A new tribe in Phrymaceae and a new family in Lamiales. J. Syst. Evol. 58: 1-17.

[114] Liu, B.B., Campbell, C.S., Hong, D.Y., and Wen, J. (2020a). Phylogenetic relationships and chloroplast capture in the Amelanchier-Malacomeles-Peraphyllum clade (Maleae, Rosaceae): Evidence from chloroplast genome and nuclear ribosomal DNA data using genome skimming. Mol. Phylogenet. Evol. 147: 106784.

[115] Liu, B.B., Ren, C., Kwak, M., Hodel, R.G.J., Xu, C., He, J., Zhou, W., Bin , Huang, C.H., Ma, H., et al. (2022). Phylogenomic conflict analyses in the apple genus Malus s.l. reveal widespread hybridization and allopolyploidy driving diversification, with insights into the complex biogeographic history in the Northern Hemisphere. J. Integr. Plant Biol. 64: 1020-1043.

[116] Liu, J., Nie, Z.-L., Ren, C., Su, C., and Wen, J. (2023). Phylogenomics of Aralia sect. Aralia (Araliaceae): Signals of hybridization and insights into its species delimitations and intercontinental biogeography. Mol. Phylogenet. Evol. 181: 107727.

[117] Liu, M., Zhang, C., Huang, C.-H., and Ma, H. (2015). Phylogenetic reconstruction of tribal relationships in Asteroideae (Asteraceae) with low-copy nuclear genes. Chinese Bull. Bot. 50: 549-564.

[118] Liu, P.L., Zhang, X., Mao, J.F., Hong, Y.M., Zhang, R.G., E, Y., Nie, S., Jia, K., Jiang, C.K., He, J., et al. (2020c). The Tetracentron genome provides insight into the early evolution of eudicots and the formation of vessel elements. Genome Biol. 21: 1-30.

[119] Lloyd Evans, D., Joshi, S.V., and Wang, J. (2019). Whole chloroplast genome and gene locus phylogenies reveal the taxonomic placement and relationship of Tripidium (Panicoideae: Andropogoneae) to sugarcane. BMC Evol. Biol. 19: 1-20.

[120] Loiseau, O., Mota Machado, T., Paris, M., Koubínová, D., Dexter, K.G., Versieux, L.M., Lexer, C., and Salamin, N. (2021). Genome skimming reveals widespread hybridization in a Neotropical flowering plant radiation. Front. Ecol. Evol. 9: 322.

[121] Loiseau, O., Olivares, I., Paris, M., de La Harpe, M., Weigand, A., Koubínová, D., Rolland, J., Bacon, C.D., Balslev, H., Borchsenius, F., et al. (2019). Targeted capture of hundreds of nuclear genes unravels phylogenetic relationships of the diverse neotropical palm tribe Geonomateae. Front. Plant Sci. 10: 864.

[122] Losos, J.B., Arnold, S.J., Bejerano, G., Brodie, E.D., Hibbett, D., Hoekstra, H.E., Mindell, D.P., Monteiro, A., Moritz, C., Orr, H.A., et al. (2013). Evolutionary biology for the 21st century. PLoS Biol. 11: e1001466.

[123] Lu, W.X., Hu, X.Y., Wang, Z.Z., and Rao, G.Y. (2022). Hyb-Seq provides new insights into the phylogeny and evolution of the Chrysanthemum zawadskii species complex in China. Cladistics 38: 663-683.

[124] De Luca, D., Kooistra, W.H.C.F., Sarno, D., Biffali, E., and Piredda, R. (2021). Empirical evidence for concerted evolution in the 18S rDNA region of the planktonic diatom genus Chaetoceros. Sci. Rep. 11: 1-11.

[125] Luebert, F., Cecchi, L., Frohlich, M.W., Gottschling, M., Guilliams, C.M., Hasenstab-Lehman, K.E., Hilger, H.H., Miller, J.S., Mittelbach, M., Nazaire, M., et al. (2016). Familial classification of the boraginales. Taxon 65: 502-522.

[126] Ma, H., Lu, J., Liu, B.-B., Duan, B.-B., He, X.-D., and Liu, J.-Q. (2015). Phylotranscriptomic analyses in plants using Betulaceae as an example. J. Syst. Evol. 53: 403-410.

[127] Ma, Z.Y., Nie, Z.L., Ren, C., Liu, X.Q., Zimmer, E.A., and Wen, J. (2021). Phylogenomic relationships and character evolution of the grape family (Vitaceae). Mol. Phylogenet. Evol. 154: 106948.

[128] Mandel, J.R., Dikow, R.B., Siniscalchi, C.M., Thapa, R., Watson, L.E., and Funk, V.A. (2019). A fully resolved backbone phylogeny reveals numerous dispersals and explosive diversifications throughout the history of Asteraceae. Proc. Natl. Acad. Sci. U.S.A. 116: 14083-14088.

[129] Massatti, R., Reznicek, A.A., and Knowles, L.L. (2016). Utilizing RADseq data for phylogenetic analysis of challenging taxonomic groups: A case study in Carex sect. Racemosae. Am. J. Bot. 103: 337-347.

[130] Maurin, O., Anest, A., Bellot, S., Biffin, E., Brewer, G., Charles-Dominique, T., Cowan, R.S., Dodsworth, S., Epitawalage, N., Gallego, B., et al. (2021). A nuclear phylogenomic study of the angiosperm order Myrtales, exploring the potential and limitations of the universal Angiosperms353 probe set. Am. J. Bot. 108: 1087-1111.

[131] McGee, M.D., Borstein, S.R., Meier, J.I., Marques, D.A., Mwaiko, S., Taabu, A., Kishe, M.A., O'Meara, B., Bruggmann, R., Excoffier, L., et al. (2020). The ecological and genomic basis of explosive adaptive radiation. Nature 586: 75-79.

[132] Meerow, A.W., Gardner, E.M., and Nakamura, K. (2020). Phylogenomics of the Andean tetraploid clade of the American Amaryllidaceae (Subfamily Amaryllidoideae): Unlocking a polyploid generic radiation abetted by continental geodynamics. Front. Plant Sci. 11: 1698.

[133] Meng, K.K., Chen, S.F., Xu, K.W., Zhou, R.C., Li, M.W., Dhamala, M.K., Liao, W.B., and Fan, Q. (2021). Phylogenomic analyses based on genome-skimming data reveal cyto-nuclear discordance in the evolutionary history of Cotoneaster (Rosaceae). Mol. Phylogenet. Evol. 158: 107083.

[134] Mitchell, N., Lewis, P.O., Lemmon, E.M., Lemmon, A.R., and Holsinger, K.E. (2017). Anchored phylogenomics improves the resolution of evolutionary relationships in the rapid radiation of Protea L. Am. J. Bot. 104: 102-115.

[135] Moore, M.J., Soltis, P.S., Bell, C.D., Burleigh, J.G., and Soltis, D.E. (2010). Phylogenetic analysis of 83 plastid genes further resolves the early diversification of eudicots. Proc. Natl. Acad. Sci. U.S.A. 107: 4623.

[136] Morales-Briones, D.F., Gehrke, B., Huang, C.-H., Liston, A., Ma, H., Marx, H.E., Tank, D.C., and Yang, Y. (2021a). Analysis of paralogs in target enrichment data pinpoints multiple ancient polyploidy events in Alchemilla s.l. (Rosaceae). Syst. Biol. 71: 190-207.

[137] Morales-Briones, D.F., Kadereit, G., Tefarikis, D.T., Moore, M.J., Smith, S.A., Brockington, S.F., Timoneda, A., Yim, W.C., Cushman, J.C., and Yang, Y. (2021b). Disentangling sources of gene tree discordance in phylogenomic data sets: Testing ancient hybridizations in Amaranthaceae s.l. Syst. Biol. 70: 219-235.

[138] Morales-Briones, D.F., Liston, A., and Tank, D.C. (2018). Phylogenomic analyses reveal a deep history of hybridization and polyploidy in the Neotropical genus Lachemilla (Rosaceae). New Phytol. 218: 1668-1684.

[139] Morales-Briones, D.F., and Tank, D.C. (2019). Extensive allopolyploidy in the Neotropical genus Lachemilla (Rosaceae) revealed by PCR-based target enrichment of the nuclear ribosomal DNA cistron and plastid phylogenomics. Am. J. Bot. 106: 415-437.

[140] Mu, X.Y., Tong, L., Sun, M., Zhu, Y.X., Wen, J., Lin, Q.W., and Liu, B. (2020). Phylogeny and divergence time estimation of the walnut family (Juglandaceae) based on nuclear RAD-Seq and chloroplast genome data. Mol. Phylogenet. Evol. 147: 106802.

[141] Murillo, A.J., Valencia, D.J., Orozco, C.I., Parra, O.C., and Neubig, K.M. (2022). Incomplete lineage sorting and reticulate evolution mask species relationships in Brunelliaceae, an Andean family with rapid, recent diversification. Am. J. Bot. 109: 1139-1156.

[142] Nesse, R.M., Bergstrom, C.T., Ellison, P.T., Flier, J.S., Gluckman, P., Govindaraju, D.R., Niethammer, D., Omenn, G.S., Perlman, R.L., Schwartz, M.D., et al. (2010). Making evolutionary biology a basic science for medicine. Proc. Natl. Acad. Sci. U.S.A. 107: 1800-1807.

[143] Nicholls, J.A., Pennington, R.T., Koenen, E.J.M., Hughes, C.E., Hearn, J., Bunnefeld, L., Dexter, K.G., Stone, G.N., and Kidner, C.A. (2015). Using targeted enrichment of nuclear genes to increase phylogenetic resolution in the neotropical rain forest genus Inga (Leguminosae: Mimosoideae). Front. Plant Sci. 6: 710.

[144] Nickrent, D.L., Malécot, V., Vidal-Russell, R., and Der, J.P. (2010). A revised classification of Santalales. Taxon 59: 538-558.

[145] Ogutcen, E., Christe, C., Nishii, K., Salamin, N., Möller, M., and Perret, M. (2021). Phylogenomics of Gesneriaceae using targeted capture of nuclear genes. Mol. Phylogenet. Evol. 157: 107068.

[146] Olofsson, J.K., Cantera, I., Van de Paer, C., Hong-Wa, C., Zedane, L., Dunning, L.T., Alberti, A., Christin, P.A., and Besnard, G. (2019). Phylogenomics using low-depth whole genome sequencing: A case study with the olive tribe. Mol. Ecol. Resour. 19: 877-892.

[147] Osuna-Mascaró, C., Rubio de Casas, R., Landis, J.B., and Perfectti, F. (2021). Genomic resources for Erysimum spp. (Brassicaceae): Transcriptome and chloroplast genomes. Front. Ecol. Evol. 9: 206.

[148] Panero, J.L., and Crozier, B.S. (2016). Macroevolutionary dynamics in the early diversification of Asteraceae. Mol. Phylogenet. Evol. 99: 116-132.

[149] Panero, J.L., Freire, S.E., Ariza Espinar, L., Crozier, B.S., Barboza, G.E., and Cantero, J.J. (2014). Resolution of deep nodes yields an improved backbone phylogeny and a new basal lineage to study early evolution of Asteraceae. Mol. Phylogenet. Evol. 80: 43-53.

[150] Paulus, J.K., Schlieper, D., and Groth, G. (2013). Greater efficiency of photosynthetic carbon fixation due to single amino-acid substitution. Nat. Commun. 4: 1-7.

[151] Pérez-Escobar, O.A., Dodsworth, S., Bogarín, D., Bellot, S., Balbuena, J.A., Schley, R.J., Kikuchi, I.A., Morris, S.K., Epitawalage, N., Cowan, R., et al. (2021). Hundreds of nuclear and plastid loci yield novel insights into orchid relationships. Am. J. Bot. 108: 1166-1180.

[152] Potter, D., Eriksson, T., Evans, R.C., Oh, S., Smedmark, J.E.E., Morgan, D.R., Kerr, M., Robertson, K.R., Arsenault, M., Dickinson, T.A., et al. (2007). Phylogeny and classification of Rosaceae. Plant Syst. Evol. 266: 5-43.

[153] Pouchon, C., Fernández, A., Nassar, J.M., Boyer, F., Aubert, S., Lavergne, S., and Mavárez, J. (2018). Phylogenomic analysis of the explosive adaptive radiation of the Espeletia complex (Asteraceae) in the tropical Andes. Syst. Biol. 67: 1041-1060.

[154] Qiao, Q., Edger, P.P., Xue, L., Qiong, L., Lu, J., Zhang, Y., Cao, Q., Yocca, A.E., Platts, A.E., Knapp, S.J., et al. (2021). Evolutionary history and pan-genome dynamics of strawberry (Fragaria spp.). Proc. Natl. Acad. Sci. U.S.A. 118: e2105431118.

[155] Qiu, Y.L., Li, L., Wang, B., Xue, J.Y., Hendry, T.A., Li, R.Q., Brown, J.W., Liu, Y., Hudson, G.T., and Chen, Z.D. (2010). Angiosperm phylogeny inferred from sequences of four mitochondrial genes. J. Syst. Evol. 48: 391-425.

[156] Raza, M., Ortiz, E.M., Schwung, L., Shigita, G., and Schaefer, H. (2023). Resolving the phylogeny of Thladiantha (Cucurbitaceae) with three different targeted-capture pipelines. BMC. Ecol. Evol. 23: 75.

[157] Ren, C., Wang, L., Nie, Z.L., Johnson, G., Yang, Q.E., and Wen, J. (2021). Development and phylogenetic utilities of a new set of single-/low-copy nuclear genes in Senecioneae (Asteraceae), with new insights into the tribal position and the relationships within subtribe Tussilagininae. Mol. Phylogenet. Evol. 162: 107202.

[158] Ren, R., Wang, H., Guo, C., Zhang, N., Zeng, L., Chen, Y., Ma, H., and Qi, J. (2018). Widespread whole genome duplications contribute to genome complexity and species diversity in angiosperms. Mol. Plant 11: 414-428.

[159] Rendón-Anaya, M., Ibarra-Laclette, E., Méndez-Bravo, A., Lan, T., Zheng, C., Carretero-Paulet, L., Perez-Torres, C.A., Chacón-López, A., Hernandez-Guzmán, G., Chang, T.H., et al. (2019). The avocado genome informs deep angiosperm phylogeny, highlights introgressive hybridization, and reveals pathogen-influenced gene space adaptation. Proc. Natl. Acad. Sci. U.S.A. 116: 17081-17089.

[160] Reyes, E., Sauquet, H., and Nadot, S. (2016). Perianth symmetry changed at least 199 times in angiosperm evolution. Taxon 65: 945-964.

[161] Ringelberg, J.J., Koenen, E.J.M., Iganci, J.R., de Queiroz, L.P., Murphy, D.J., Gaudeul, M., Bruneau, A., Luckow, M., Lewis, G.P., and Hughes, C.E. (2022). Phylogenomic analysis of 997 nuclear genes reveals the need for extensive generic re-delimitation in Caesalpinioideae (Leguminosae). PhytoKeys 205: 3-58.

[162] Rose, J.P., Kriebel, R., Kahan, L., DiNicola, A., González-Gallegos, J.G., Celep, F., Lemmon, E.M., Lemmon, A.R., Sytsma, K.J., and Drew, B.T. (2021). Sage insights into the phylogeny of Salvia: Dealing with sources of discordance within and across genomes. Front. Plant Sci. 12: 2606.

[163] Roy, S., Liu, W., Nandety, R.S., Crook, A., Mysore, K.S., Pislariu, C.I., Frugoli, J., Dickstein, R., and Udvardi, M.K. (2020). Celebrating 20 years of genetic discoveries in legume nodulation and symbiotic nitrogen fixation. Plant Cell 32: 15-41.

[164] Ruhfel, B.R., Gitzendanner, M.A., Soltis, P.S., Soltis, D.E., and Burleigh, J.G. (2014). From algae to angiosperms-inferring the phylogeny of green plants (Viridiplantae) from 360 plastid genomes. BMC Evol. Biol. 14: 1-27.

[165] Sage, R.F. (2004). The evolution of C4 photosynthesis. New Phytol. 161: 341-370.

[166] Särkinen, T., Bohs, L., Olmstead, R.G., and Knapp, S. (2013). A phylogenetic framework for evolutionary study of the nightshades (Solanaceae): A dated 1,000-tip tree. BMC Evol. Biol. 13: 1-15.

[167] Sass, C., Iles, W.J.D., Barrett, C.F., Smith, S.Y., and Specht, C.D. (2016). Revisiting the Zingiberales: Using multiplexed exon capture to resolve ancient and recent phylogenetic splits in a charismatic plant lineage. PeerJ 2016: e1584.

[168] Sauquet, H., Balthazar, M., von Magallón, S., Doyle, J.A., Endress, P.K., Bailes, E.J., Morais, E.B., de Bull-Hereñu, K., Carrive, L., Chartier, M., et al. (2017). The ancestral flower of angiosperms and its early diversification. Nat. Commun. 8: 1-10.

[169] Schmickl, R., Liston, A., Zeisek, V., Oberlander, K., Weitemier, K., Straub, S.C.K., Cronn, R.C., Dreyer, L.L., and Suda, J. (2016). Phylogenetic marker development for target enrichment from transcriptome and genome skim data: The pipeline and its application in southern African Oxalis (Oxalidaceae). Mol. Ecol. Resour. 16: 1124-1135.

[170] Schneider, J.V., Jungcurt, T., Cardoso, D., Amorim, A.M., Töpel, M., Andermann, T., Poncy, O., Berberich, T., and Zizka, G. (2021a). Phylogenomics of the tropical plant family Ochnaceae using targeted enrichment of nuclear genes and 250+ taxa. Taxon 70: 48-71.

[171] Schneider, J.V., Paule, J., Jungcurt, T., Cardoso, D., Amorim, A.M., Berberich, T., and Zizka, G. (2021b). Resolving recalcitrant clades in the pantropical Ochnaceae: Insights from comparative phylogenomics of plastome and nuclear genomic data derived from targeted sequencing. Front. Plant Sci. 12: 105.

[172] Serna-Sánchez, M.A., Pérez-Escobar, O.A., Bogarín, D., Torres-Jimenez, M.F., Alvarez-Yela, A.C., Arcila-Galvis, J.E., Hall, C.F., de Barros, F., Pinheiro, F., Dodsworth, S., et al. (2021). Plastid phylogenomics resolves ambiguous relationships within the orchid family and provides a solid timeframe for biogeography and macroevolution. Sci. Rep. 11: 1-11.

[173] Siniscalchi, C.M., Correa-Narvaez, J., Kates, H.R., Soltis, D.E., Soltis, P.S., Guralnick, R.P., Manchester, S.R., and Folk, R.A. (2023). Fagalean phylogeny in a nutshell: Chronicling the diversification history of Fagales. bioRxiv.

[174] Siniscalchi, C.M., Loeuille, B., Funk, V.A., Mandel, J.R., and Pirani, J.R. (2019). Phylogenomics yields new insight into relationships within Vernonieae (Asteraceae). Front. Plant Sci. 10: 1224.

[175] Smith, M.L., and Hahn, M.W. (2022). The frequency and topology of pseudoorthologs. Syst. Biol. 71: 649-659.

[176] Soltis, D.E., Smith, S.A., Cellinese, N., Wurdack, K.J., Tank, D.C., Brockington, S.F., Refulio-Rodriguez, N.F., Walker, J.B., Moore, M.J., Carlsward, B.S., et al. (2011). Angiosperm phylogeny: 17 genes, 640 taxa. Am. J. Bot. 98: 704-730.

[177] Soltis, D.E., Soltis, P.S., Chase, M.W., Mort, M.E., Albach, D.C., Zanis, M., Savolainen, V., Hahn, W.H., Hoot, S.B., Fay, M.F., et al. (2000). Angiosperm phylogeny inferred from 18S rDNA, rbcL, and atpB sequences. Bot. J. Linn. Soc. 133: 381-461.

[178] Soltis, P.S., Folk, R.A., and Soltis, D.E. (2019). Darwin review: Angiosperm phylogeny and evolutionary radiations. Proc. R. Soc. B 286: 20190099.

[179] Soreng, R.J., Peterson, P.M., Romaschenko, K., Davidse, G., Teisher, J.K., Clark, L.G., Barberá, P., Gillespie, L.J., and Zuloaga, F.O. (2017). A worldwide phylogenetic classification of the Poaceae (Gramineae) II: An update and a comparison of two 2015 classifications. J. Syst. Evol. 55: 259-290.

[180] Soreng, R.J., Peterson, P.M., Romaschenko, K., Davidse, G., Zuloaga, F.O., Judziewicz, E.J., Filgueiras, T.S., Davis, J.I., and Morrone, O. (2015). A worldwide phylogenetic classification of the Poaceae (Gramineae). J. Syst. Evol. 53: 117-137.

[181] Soto Gomez, M., Pokorny, L., Kantar, M.B., Forest, F., Leitch, I.J., Gravendeel, B., Wilkin, P., Graham, S.W., and Viruel, J. (2019). A customized nuclear target enrichment approach for developing a phylogenomic baseline for Dioscorea yams (Dioscoreaceae). Appl. Plant Sci. 7: e11254.

[182] Sousa-Baena, M.S., Sinha, N.R., Hernandes-Lopes, J., and Lohmann, L.G. (2018). Convergent evolution and the diverse ontogenetic origins of tendrils in angiosperms. Front. Plant Sci. 9: 403.

[183] Stefanović, S., Rice, D.W., and Palmer, J.D. (2004). Long branch attraction, taxon sampling, and the earliest angiosperms: Amborella or monocots? BMC Evol. Biol. 4: 1-35.

[184] Stetter, M.G., and Schmid, K.J. (2017). Analysis of phylogenetic relationships and genome size evolution of the Amaranthus genus using GBS indicates the ancestors of an ancient crop. Mol. Phylogenet. Evol. 109: 80-92.

[185] Stubbs, R.L., Folk, R.A., Xiang, C.L., Chen, S., Soltis, D.E., and Cellinese, N. (2020). A phylogenomic perspective on evolution and discordance in the alpine-arctic plant clade Micranthes (Saxifragaceae). Front. Plant Sci. 10: 1773.

[186] Stubbs, R.L., Folk, R.A., Xiang, C.L., Soltis, D.E., and Cellinese, N. (2018). Pseudo-parallel patterns of disjunctions in an Arctic-alpine plant lineage. Mol. Phylogenet. Evol. 123: 88-100.

[187] Suzuki, W., Konishi, M., and Yanagisawa, S. (2013). The evolutionary events necessary for the emergence of symbiotic nitrogen fixation in legumes may involve a loss of nitrate responsiveness of the NIN transcription factor. Plant Signal. Behav. 8: e25975.

[188] Takahashi, K., Terai, Y., Nishida, M., and Okada, N. (2001). Phylogenetic relationships and ancient incomplete lineage sorting among cichlid fishes in lake Tanganyika as revealed by analysis of the insertion of retroposons. Mol. Biol. Evol. 18: 2057-2066.

[189] Tamura, M.N., Yamashita, J., Fuse, S., and Haraguchi, M. (2004). Molecular phylogeny of monocotyledons inferred from combined analysis of plastid matK and rbcL gene sequences. J. Plant Res. 117: 109-120.

[190] Tang, C.Y., Li, S., Wang, Y.T., and Wang, X. (2020). Comparative genome/transcriptome analysis probes Boraginales’ phylogenetic position, WGDs in Boraginales, and key enzyme genes in the alkannin/shikonin core pathway. Mol. Ecol. Resour. 20: 228-241.

[191] Tang, D., Jia, Y., Zhang, J., Li, H., Cheng, L., Wang, P., Bao, Z., Liu, Z., Feng, S., Zhu, X., et al. (2022). Genome evolution and diversity of wild and cultivated potatoes. Nature 606: 535-541.

[192] Thomas, A.E., Igea, J., Meudt, H.M., Albach, D.C., Lee, W.G., and Tanentzap, A.J. (2021a). Using target sequence capture to improve the phylogenetic resolution of a rapid radiation in New Zealand Veronica. Am. J. Bot. 108: 1289-1306.

[193] Thomas, S.K., Liu , Xiang, D.Z.-Y., Dong, Y., Cummings, A., Pokorny, L., Xiang, Q.-Y., Leebens-Mack, J.H., Liu, X., Du, Z., et al. (2021b). Comprehending Cornales: Phylogenetic reconstruction of the order using the Angiosperms353 probe set. Am. J. Bot. 108: 1112-1121.

[194] Thureborn, O., Razafimandimbison, S.G., Wikström, N., and Rydin, C. (2022). Target capture data resolve recalcitrant relationships in the coffee family (Rubioideae, Rubiaceae). Front. Plant Sci. 13: 967456.

[195] Timilsena, P.R., Wafula, E.K., Barrett, C.F., Ayyampalayam, S., McNeal, J.R., Rentsch, J.D., McKain, M.R., Heyduk, K., Harkess, A., Villegente, M., et al. (2022). Phylogenomic resolution of order- and family-level monocot relationships using 602 single-copy nuclear genes and 1375 BUSCO genes. Front. Plant Sci. 13: 4140.

[196] Unruh, S.A., Mckain, M.R., Lee, Y.-I.Y.-I., Yukawa, T., Mccormick, M.K., Shefferson, R.P., Smithson, A., Leebens-Mack, J.H., Pires, J.C., Mckain, M.R., et al. (2018). Phylotranscriptomic analysis and genome evolution of the Cypripedioideae (Orchidaceae). Am. J. Bot. 105: 631-640.

[197] Uribe-Convers, S., Settles, M.L., and Tank, D.C. (2016). A phylogenomic approach based on PCR target enrichment and high throughput sequencing: Resolving the diversity within the south American species of Bartsia L. (Orobanchaceae). PLoS ONE 11: e0148203.

[198] Vargas, O.M., Heuertz, M., Smith, S.A., and Dick, C.W. (2019). Target sequence capture in the Brazil nut family (Lecythidaceae): Marker selection and in silico capture from genome skimming data. Mol. Phylogenet. Evol. 135: 98-104.

[199] Vargas, O.M., Ortiz, E.M., and Simpson, B.B. (2017). Conflicting phylogenomic signals reveal a pattern of reticulate evolution in a recent high-Andean diversification (Asteraceae: Astereae: Diplostephium). New Phytol. 214: 1736-1750.

[200] Villaverde, T., Jiménez-Mejías, P., Luceño, M., Waterway, M.J., Kim, S., Lee, B., Rincón-Barrado, M., Hahn, M., Maguilla, E., Roalson, E.H., et al. (2020). A new classification of Carex (Cyperaceae) subgenera supported by a HybSeq backbone phylogenetic tree. Bot. J. Linn. Soc. 194: 141-163.

[201] Villaverde, T., Pokorny, L., Olsson, S., Rincón-Barrado, M., Johnson, M.G., Gardner, E.M., Wickett, N.J., Molero, J., Riina, R., and Sanmartín, I. (2018). Bridging the micro- and macroevolutionary levels in phylogenomics: Hyb-Seq solves relationships from populations to species and above. New Phytol. 220: 636-650.

[202] Walker, J.F., Yang, Y., Moore, M.J., Mikenas, J., Timoneda, A., Brockington, S.F., and Smith, S.A. (2017). Widespread paleopolyploidy, gene tree conflict, and recalcitrant relationships among the carnivorous Caryophyllales. Am. J. Bot. 104: 858-867.

[203] Wang, M., Zhang, L., Zhang, Z., Li, M., Wang, D., Zhang, X., Xi, Z., Keefover-Ring, K., Smart, L.B., DiFazio, S.P., et al. (2020). Phylogenomics of the genus Populus reveals extensive interspecific gene flow and balancing selection. New Phytol. 225: 1370-1382.

[204] Wang, S., Yang, X., Xu, M., Lin, X., Lin, T., Qi, J., Shao, G., Tian, N., Yang, Q., Zhang, Z., et al. (2015). A rare SNP identified a TCP transcription factor essential for tendril development in cucumber. Mol. Plant 8: 1795-1808.

[205] Wang, W., Zhang, X., Garcia, S., Leitch, A.R., and Kovařík, A. (2023a). Intragenomic rDNA variation - the product of concerted evolution, mutation, or something in between? Heredity 131: 179-188.

[206] Wang, X., Ye, X., Zhao, L., Li, D., Guo, Z., and Zhuang, H. (2017). Genome-wide RAD sequencing data provide unprecedented resolution of the phylogeny of temperate bamboos (Poaceae: Bambusoideae). Sci. Rep. 7: 1-11.

[207] Wang, Y., Hao, G.Q., Guo, X.Y., Zhang, D., Hu, Q.J., and Liu, J.Q. (2023b). Phylogenomics and rapid diversification of the genus Eutrema on the Qinghai-Tibet Plateau and adjacent regions. J. Syst. Evol. 61: 11-21.

[208] Wang, Y., Huang, J., Li, E., Xu, S., Zhan, Z., Zhang, X., Yang, Z., Guo, F., Liu, K., Liu, D., et al. (2022a). Phylogenomics and biogeography of Populus based on comprehensive sampling reveal deep-level relationships and multiple intercontinental dispersals. Front. Plant Sci. 13: 8.

[209] Wang, Z., Li, Y., Sun, P., Zhu, M., Wang, D., Lu, Z., Hu, H., Xu, R., Zhang, J., Ma, J., et al. (2022b). A high-quality Buxus austro-yunnanensis (Buxales) genome provides new insights into karyotype evolution in early eudicots. BMC Biol. 20: 1-17.

[210] Wanke, S., Granados Mendoza, C., Müller, S., Paizanni Guillén, A., Neinhuis, C., Lemmon, A.R., Lemmon, E.M., and Samain, M.S. (2017). Recalcitrant deep and shallow nodes in Aristolochia (Aristolochiaceae) illuminated using anchored hybrid enrichment. Mol. Phylogenet. Evol. 117: 111-123.

[211] Washburn, J.D., Schnable, J.C., Conant, G.C., Brutnell, T.P., Shao, Y., Zhang, Y., Ludwig, M., Davidse, G., and Pires, J.C. (2017). Genome-guided phylo-transcriptomic methods and the nuclear phylogentic tree of the Paniceae grasses. Sci. Rep. 7: 1-12.

[212] Watson, L.E., Siniscalchi, C.M., and Mandel, J. (2020). Phylogenomics of the hyperdiverse daisy tribes: Anthemideae, Astereae, Calenduleae, Gnaphalieae, and Senecioneae. J. Syst. Evol. 58: 841-852.

[213] Wen, J., Yu, Y., Xie, D.F., Peng, C., Liu, Q., Zhou, S.D., and He, X.J. (2020). A transcriptome-based study on the phylogeny and evolution of the taxonomically controversial subfamily Apioideae (Apiaceae). Ann. Bot. 125: 937-953.

[214] Wong, D.C.J., and Peakall, R. (2022). Orchid phylotranscriptomics: The prospects of repurposing multi-tissue transcriptomes for phylogenetic analysis and beyond. Front. Plant Sci. 13: 910362.

[215] Worberg, A., Quandt, D., Barniske, A.M., Löhne, C., Hilu, K.W., and Borsch, T. (2007). Phylogeny of basal eudicots: Insights from non-coding and rapidly evolving DNA. Org. Divers. Evol. 7: 55-77.

[216] Wu, F.Y., Tang, C.Y., Guo, Y.M., Bian, Z.W., Fu, J.Y., Lu, G.H., Qi, J.L., Pang, Y.J., and Yang, Y.H. (2017). Transcriptome analysis explores genes related to shikonin biosynthesis in Lithospermeae plants and provides insights into Boraginales’ evolutionary history. Sci. Rep. 7: 1-11.

[217] Wurdack, K.J., and Davis, C.C. (2009). Malpighiales phylogenetics: Gaining ground on one of the most recalcitrant clades in the angiosperm tree of life. Am. J. Bot. 96: 1551-1570.

[218] Xi, Z., Ruhfel, B.R., Schaefer, H., Amorim, A.M., Sugumaran, M., Wurdack, K.J., Endress, P.K., Matthews, M.L., Stevens, P.F., Mathews, S., et al. (2012). Phylogenomics and a posteriori data partitioning resolve the Cretaceous angiosperm radiation Malpighiales. Proc. Natl. Acad. Sci. U.S.A. 109: 17519-17524.

[219] Xia, X.M., Yang, M.Q., Li, C.L., Huang, S.X., Jin, W.T., Shen, T.T., Wang, F., Li, X.H., Yoichi, W., Zhang, L.H., et al. (2022). Spatiotemporal evolution of the global species diversity of rhododendron. Mol. Biol. Evol. 39: msab314.

[220] Xiang, Q.Y. (Jenny ), Thomas, D.T., and Xiang, Q.P. (2011). Resolving and dating the phylogeny of Cornales—Effects of taxon sampling, data partitions, and fossil calibrations. Mol. Phylogenet. Evol. 59: 123-138.

[221] Xiang, Y., Huang, C.H., Hu, Y., Wen, J., Li, S., Yi, T., Chen, H., Xiang, J., and Ma, H. (2017). Evolution of Rosaceae fruit types based on nuclear phylogeny in the context of geological times and genome duplication. Mol. Biol. Evol. 34: 262-281.

[222] Xiong, H., Wang, D., Shao, C., Yang, X., Yang, J., Ma, T., Davis, C.C., Liu, L., and Xi, Z. (2022). Species tree estimation and the impact of gene loss following whole-genome duplication. Syst. Biol. 71: 1348-1361.

[223] Xue, B., Guo, X., Landis, J.B., Sun, M., Tang, C.C., Soltis, P.S., Soltis, D.E., and Saunders, R.M.K. (2020). Accelerated diversification correlated with functional traits shapes extant diversity of the early divergent angiosperm family Annonaceae. Mol. Phylogenet. Evol. 142: 106659.

[224] Yang, J.W., Qin, X.M., Xu, J., Li, C.R., Ren, Q.F., Yuan, M.Q., Zhang, Q., Yi, S.R., and Cai, L. (2022). Oreocharis qianyuensis, a new species of Gesneriaceae from Southwest, China based on morphological and molecular evidence. PhytoKeys 213: 119-130.

[225] Yang, L., Su, D., Chang, X., Foster, C.S.P., Sun, L., Huang, C.H., Zhou, X., Zeng, L., Ma, H., and Zhong, B. (2020a). Phylogenomic insights into deep phylogeny of angiosperms based on broad nuclear gene sampling. Plant Commun. 1: 100027.

[226] Yang, X., Yan, J., Zhang, Z.hen, Lin, T., Xin, T., Wang, B., Wang, S., Zhao, J., Zhang, Z.honghua, Lucas, W.J., et al. (2020b). Regulation of plant architecture by a new histone acetyltransferase targeting gene bodies. Nat. Plants 6: 809-822.

[227] Yang, Y., Moore, M.J., Brockington, S.F., Mikenas, J., Olivieri, J., Walker, J.F., and Smith, S.A. (2018). Improved transcriptome sampling pinpoints 26 ancient and more recent polyploidy events in Caryophyllales, including two allopolyploidy events. New Phytol. 217: 855-870.

[228] Yang, Y., Moore, M.J., Brockington, S.F., Soltis, D.E., Wong, G.K.S., Carpenter, E.J., Zhang, Y., Chen, L., Yan, Z., Xie, Y., et al. (2015). Dissecting molecular evolution in the highly diverse plant clade Caryophyllales using transcriptome sequencing. Mol. Biol. Evol. 32: 2001-2014.

[229] Yang, Y., and Smith, S.A. (2014). Orthology inference in nonmodel organisms using transcriptomes and low-coverage genomes: Improving accuracy and matrix occupancy for phylogenomics. Mol. Biol. Evol. 31: 3081-3092.

[230] Yang, Y., Sun, P., Lv, L., Wang, D., Ru, D., Li, Y., Ma, T., Zhang, L., Shen, X., Meng, F., et al. (2020c). Prickly waterlily and rigid hornwort genomes shed light on early angiosperm evolution. Nat. Plants 6: 215-222.

[231] Yang, Y.Y., Qu, X.J., Zhang, R., Stull, G.W., and Yi, T.S. (2021). Plastid phylogenomic analyses of Fagales reveal signatures of conflict and ancient chloroplast capture. Mol. Phylogenet. Evol. 163: 107232.

[232] Yao, G., Zhang, Y.Q., Barrett, C., Xue, B., Bellot, S., Baker, W.J., and Ge, X.J. (2023). A plastid phylogenomic framework for the palm family (Arecaceae). BMC Biol. 21: 50.

[233] Yoo, M.J., Lee, B.Y., Kim, S., and Lim, C.E. (2021). Phylogenomics with Hyb-Seq unravels Korean Hosta evolution. Front. Plant Sci. 12: 1398.

[234] Zanis, M.J., Soltis, D.E., Soltis, P.S., Mathews, S., and Donoghue, M.J. (2002). The root of the angiosperms revisited. Proc. Natl. Acad. Sci. U.S.A. 99: 6848-6853.

[235] Zeng, L., Zhang, N., Zhang, Q., Endress, P.K., Huang, J., and Ma, H. (2017). Resolution of deep eudicot phylogeny and their temporal diversification using nuclear genes from transcriptomic and genomic datasets. New Phytol. 214: 1338-1354.

[236] Zeng, L., Zhang, Q., Sun, R., Kong, H., Zhang, N., and Ma, H. (2014). Resolution of deep angiosperm phylogeny using conserved nuclear genes and estimates of early divergence times. Nat. Commun. 5: 4956.

[237] Zhai, W., Duan, X., Zhang, R., Guo, C., Li, L., Xu, G., Shan, H., Kong, H., and Ren, Y. (2019). Chloroplast genomic data provide new and robust insights into the phylogeny and evolution of the Ranunculaceae. Mol. Phylogenet. Evol. 135: 12-21.

[238] Zhang, C., Huang, C.-H., Liu, M., Hu, Y., Panero, J.L., Luebert, F., Gao, T., and Ma, H. (2021). Phylotranscriptomic insights into Asteraceae diversity, polyploidy, and morphological innovation. J. Integr. Plant Biol. 63: 1273-1293.

[239] Zhang, C., Rabiee, M., Sayyari, E., and Mirarab, S. (2018). ASTRAL-III: Polynomial time species tree reconstruction from partially resolved gene trees. BMC Bioinformatics 19: 153.

[240] Zhang, C., Zhang, T., Luebert, F., Xiang, Y., Huang, C.H., Hu, Y., Rees, M., Frohlich, M.W., Qi, J., Weigend, M., et al. (2020a). Asterid phylogenomics/phylotranscriptomics uncover morphological evolutionary histories and support phylogenetic placement for numerous whole-genome duplications. Mol. Biol. Evol. 37: 3188-3210.

[241] Zhang, G., Hu, Y., Huang, M., Huang, W.-C., Liu, D., Zhang, D., Hu, H., Downing, J.L., Liu, Z.-J., and Ma, H. (2023a). Comprehensive phylogenetic analyses of Orchidaceae using nuclear genes and evolutionary insights into epiphytism. J. Integr. Plant Biol. 65: 1204-1225.

[242] Zhang, L., Chen, F.ei, Zhang, X., Li, Z., Zhao, Y., Lohaus, R., Chang, X., Dong, W., Ho, S.Y.W., Liu, X., et al. (2020b). The water lily genome and the early evolution of flowering plants. Nature 577: 79-84.

[243] Zhang, L., Morales-Briones, D.F., Li, Y., Zhang, G., Zhang, T., Huang, C., Guo, P., Zhang, K., Wang, Y., Wang, H., et al. (2023b). Phylogenomics insights into gene evolution, rapid species diversification, and morphological innovation of the apple tribe (Maleae, Rosaceae). New Phytol. 240: 2102-2120.

[244] Zhang, L., Wu, S., Chang, X., Wang, X., Zhao, Y., Xia, Y., Trigiano, R.N., Jiao, Y., and Chen, F. (2020c). The ancient wave of polyploidization events in flowering plants and their facilitated adaptation to environmental stress. Plant Cell Environ. 43: 2847-2856.

[245] Zhang, L., Wu, W., Yan, H.F., and Ge, X.J. (2016). Phylotranscriptomic analysis based on coalescence was less influenced by the evolving rates and the number of genes: A case study in Ericales. Evol. Bioinform. 11: 81-91.

[246] Zhang, L., Zhu, X., Zhao, Y., Guo, J., Zhang, T., Huang, W., Huang, J., Hu, Y., Huang, C.-H., and Ma, H. (2022a). Phylotranscriptomics resolves the phylogeny of Pooideae and uncovers factors for their adaptive evolution. Mol. Biol. Evol. 39: msac026.

[247] Zhang, N., Wen, J., and Zimmer, E.A. (2015). Congruent deep relationships in the grape family (Vitaceae) based on sequences of chloroplast genomes and mitochondrial genes via genome skimming. PLoS ONE 10: e0144701.

[248] Zhang, N., Zeng, L., Shan, H., and Ma, H. (2012). Highly conserved low-copy nuclear genes as effective markers for phylogenetic analyses in angiosperms. New Phytol. 195: 923-937.

[249] Zhang, Q., Zhao, L., Folk, R.A., Zhao, J.L., Zamora, N.A., Yang, S.X., Soltis, D.E., Soltis, P.S., Gao, L.M., Peng, H., et al. (2022b). Phylotranscriptomics of Theaceae: Generic-level relationships, reticulation and whole-genome duplication. Ann. Bot. 129: 457-471.

[250] Zhao, L., Li, X., Zhang, N., Zhang, S.D., Yi, T.S., Ma, H., Guo, Z.H., and Li, D.Z. (2016). Phylogenomic analyses of large-scale nuclear genes provide new insights into the evolutionary relationships within the rosids. Mol. Phylogenet. Evol. 105: 166-176.

[251] Zhao, L., Yang, Y.Y., Qu, X.J., Ma, H., Hu, Y., Li, H.T., Yi, T.S., and Li, D.Z. (2023). Phylotranscriptomic analyses reveal multiple whole-genome duplication events, the history of diversification and adaptations in the Araceae. Ann. Bot. 131: 199-214.

[252] Zhao, Y., Zhang, R., Jiang, K.W., Qi, J., Hu, Y., Guo, J., Zhu, R., Zhang, T., Egan, A.N., Yi, T.S., et al. (2021). Nuclear phylotranscriptomics and phylogenomics support numerous polyploidization events and hypotheses for the evolution of rhizobial nitrogen-fixing symbiosis in Fabaceae. Mol. Plant 14: 748-773.

[253] Zhou, B.F., Yuan, S., Crowl, A.A., Liang, Y.Y., Shi, Y., Chen, X.Y., An, Q.Q., Kang, M., Manos, P.S., and Wang, B. (2022a). Phylogenomic analyses highlight innovation and introgression in the continental radiations of Fagaceae across the Northern Hemisphere. Nat. Commun. 13: 1-14.

[254] Zhou, W., Soghigian, J., and Xiang, Q.-Y. (2022b). A new pipeline for removing paralogs in target enrichment data. Syst. Biol. 71: 410-425.

[255] Zimmer, E.A., and Wen, J. (2012). Using nuclear gene data for plant phylogenetics: Progress and prospects. Mol. Phylogenet. Evol. 65: 774-785.

[256] Zimmer, E.A., and Wen, J. (2015). Using nuclear gene data for plant phylogenetics: Progress and prospects II. Next-gen approaches. J. Syst. Evol. 53: 371-379.

[257] Zotz, G., and Hietz, P. (2001). The physiological ecology of vascular epiphytes: Current knowledge, open questions. J. Exp. Bot. 52: 2067-2078.

[258] Zotz, G., Weigelt, P., Kessler, M., Kreft, H., and Taylor, A. (2021). EpiList 1.0: A global checklist of vascular epiphytes. Ecology 102: e03326.

RIGHTS & PERMISSIONS

2024 2024 The Authors. Journal of Integrative Plant Biology published by John Wiley & Sons Australia, Ltd on behalf of Institute of Botany, Chinese Academy of Sciences.