Search

Hybridization has the potential to generate or homogenize biodiversity and is a particularly common phenomenon in plants, with an estimated 25% of species undergoing inter-specific gene flow. However, hybridization in Amazonia’s megadiverse tree flora was assumed to be extremely rare despite extensive sympatry between closely related species, and its role in diversification remains enigmatic because it has not yet been examined empirically. Using members of a dominant Amazonian tree family (Brownea, Fabaceae) as a model to address this knowledge gap, our study recovered extensive evidence of hybridization among multiple lineages across phylogenetic scales. More specifically, our results uncovered several historical introgression events betweenBrownealineages and indicated that gene tree incongruence inBrowneais best explained by introgression, rather than solely by incomplete lineage sorting. Furthermore, investigation of recent hybridization using ∼19,000 ddRAD loci recovered a high degree of shared variation between twoBrowneaspecies which co-occur in the Ecuadorian Amazon. Our analyses also showed that these sympatric lineages exhibit homogeneous rates of introgression among loci relative to the genome-wide average, implying a lack of selection against hybrid genotypes and a persistence of hybridization over time. Our results demonstrate that gene flow between multiple Amazonian tree species has occurred across temporal scales, and contrasts with the prevailing view of hybridization’s rarity in Amazonia. Overall, our results provide novel evidence that reticulate evolution influenced diversification in part of the Amazonian tree flora, which is the most diverse on Earth.

Hybridization can facilitate both evolutionary diversification and extinction and has had a critical role in plant evolution, with c. 25% of species known to hybridize in some temperate floras. However, in the species-rich Neotropical flora, the role of hybridization in the evolution of diversity remains unclear. Our review examines studies of hybridization in seed plants from across the Neotropics and explores its outcomes on Neotropical plant evolution. We review studies on a per-biome basis and a spectrum of evolutionary outcomes from hybridization are evident across Neotropical biomes and taxa. These range from short-term impacts, such as the broadening of ecological amplitude in hybrid progeny with transgressive phenotypes and genetic swamping, through to long term impacts, such as the generation of new lineages. Among these studies certain themes emerge, such as the pervasive hybridization among species-rich plant radiations from the Andean páramos, suggesting a role for hybridization in rapid diversification events. Finally, we highlight that hybridization is relatively understudied in the Neotropical flora, despite its remarkable species richness. The advent of genomic techniques can facilitate the study of hybridization and its effects in understudied biomes and plant groups. The increasing availability of genomic resources will eventually allow comparisons between tropical and temperate floras and therefore shed light on the evolutionary impacts of hybridization across the latitudinal biodiversity gradient.

Genome size varies 2400-fold across plants, influencing their evolution through changes in cell size and cell division rates which impact plants' environmental stress tolerance. Repetitive element expansion explains much genome size diversity, and the processes structuring repeat "communities" are analogous to those structuring ecological communities. However, which environmental stressors influence repeat community dynamics has not yet been examined from an ecological perspective. We measured genome size and leveraged climatic data for 91% of genera within the ecologically diverse palm family (Arecaceae). We then generated genomic repeat profiles for 141 palm species, and analysed repeats using phylogenetically informed linear models to explore relationships between repeat dynamics and environmental factors. We show that palm genome size and repeat "community" composition are best explained by aridity. Specifically, Ty3-gypsy and TIR elements were more abundant in palm species from wetter environments, which generally had larger genomes, suggesting amplification. By contrast, Ty1-copia and LINE elements were more abundant in drier environments. Our results suggest that water stress inhibits repeat expansion through selection on upper genome size limits. However, elements that may associate with stress-response genes (e.g. Ty1-copia) have amplified in arid-adapted palm species. Overall, we provide novel evidence of climate influencing the assembly of repeat "communities"., JP was supported by a Ramón y Cajal Fellowship (RYC-2017-2274) funded by MCIN/AEI/10.13039/501100011033 and by ‘ESF Investing in your future’. SB was funded by a Garfield Weston Foundation postdoctoral fellowship. PN and JM were supported by the ELIXIR CZ Research Infrastructure Project (Czech Ministry of Education, Youth and Sports; grant no. LM2018131)., IntroductionMaterials and Methods Plant material collection and genome size measurement Phylogenetic, environmental and genomic data collection Modelling relationships between genome size and environmental variables DNA repeat profiling Assessing repeat dynamics in palm genomesResults Palm genome size variation Aridity preferences of palm species help explain genome size variation Ecological metrics of palm repeat ‘communities’ vary with genome size Repeat abundances correlate with genome size Aridity preferences of palm species explain abundances of certain repeat lineagesDiscussion Palm genome size variation Aridity thresholds best explain palm genome size diversity The ‘community ecology’ of repeats correlates with genome size Repeat dynamics may be modulated by aridityConclusionsAcknowledgementsAuthor contributions

Pérez-Escobar, Oscar Alejandro, Dodsworth, Steven, Bogarín, Diego, Bellot, Sidonie, Balbuena, Juan A, Schley, Rowan J, Kikuchi, Izai A, Morris, Sarah K, Epitawalage, Niroshini, Cowan, Robyn, Maurin, Olivier, Zuntini, Alexandre, Arias, Tatiana, Serna-Sánchez, Alejandra, Gravendeel, Barbara, Torres Jimenez, Maria Fernanda, Nargar, Katharina, Chomicki, Guillaume, Chase, Mark W, Leitch, Ilia J, Forest, Félix, Baker, William J (2021): Hundreds of nuclear and plastid loci yield novel insights into orchid relationships. American journal of botany 108 (7): 1166-1180, DOI: http://doi.org/10.5281/zenodo.7778176, {"references": ["APG IV. 2016. An update of the Angiosperm Phylogeny Group classification for the orders and families of flowering plants: APG IV. Botanical Journal of the Linnean Society 181: 1-20.", "Arditti, J., and A. K. A. Ghani. 2000. Numerical and physical properties of orchid seeds and their biological implications. New Phytologist 145: 367-421.", "Bailey, C. D., T. G. Carr, S. A. Harris, and C. E. Hughes. 2003. Characterization of angiosperm nrDNA polymorphism, paralogy, and pseudogenes. Molecular Phylogenetics and Evolution 29: 435-455.", "Baker, W. J., P. Bailey, V. Barber, A. Barker, S. Bellot, D. Bishop, L. Botigue, etal. 2021. Acomprehensive platform for exploring the angiosperm tree of life. Systematic Biology syab035. https://doi.org/10.1093/sysbio/syab035.", "Balbuena, J.A., R. Miguez-Lozano, and I. Blasco-Costa. 2013. PACo: a novel procrustes application to cophylogenetic analysis. PLoS One 8: e61048.", "Balbuena, J. A., O. A. Perez-Escobar, C. Llopis-Belenguer, and I. Blasco-Costa. 2020. Random Tanglegram Partitions (Random TaPas): an Alexandrian approach to the cophylogenetic Gordian knot. Systematic Biology 69: 1212.", "Baldwin, B. G. 1992. Phylogenetic utility of the internal transcribed spacers of nuclear ribosomal DNA in plants: an example from the compositae. Molecular Phylogenetics and Evolution 1: 3-16.", "Baldwin, B. G., and S. Markos. 1998. Phylogenetic utility of the external transcribed spacer (ETS) of 18S-26S rDNA: congruence of ETS and ITS trees of Calycadenia (Compositae). Molecular Phylogenetics and Evolution 10: 449-463.", "Baldwin, B.G., M.J.Sanderson, J.M. Porter,M.F.Wojciechowski,C.S. Campbell, and M. J.Donoghue.1995. The ITS region of nuclear ribosomal DNA:a valuable source of evidence on angiosperm phylogeny. Annals of the Missouri Botanical Garden 82: 247-277.", "Bankevich, A., S. Nurk, D. Antipov, A. A. Gurevich, M. Dvorkin, A. S. Kulikov, V. M. Lesin, et al. 2012. SPAdes: A new genome assembly algorithm and its applications to single-cell sequencing. Journal of Computational Biology 19: 455-477.", "Barthlott, W., B. Grosse-Veldmann, and N. Korotkova. 2014. Orchid seed diversity: a scanning electron microscopy survey. Englera 32. Botanic Garden and Botanical Museum Berlin, Berlin, Germany.", "Bateman, R. M., P.J.Rudall, A.R. Murphy, R. S. Cowa, D. S. Devey, and O. PerezEscobar. 2021. Whole plastomes are not enough: phylogenomic and morphometric exploration at multiple demographic levels of the bee orchid clade Ophyrs sect. Sphegodes. Journal of Experimental Botany 72: 654-681.", "Bateman, R. M., G. Sramko, and O. Paun. 2018. Integrating restriction siteassociated DNA sequencing (RAD-seq) with morphological cladistic analysis clarifies evolutionary relationships among major species groups of bee orchids. Annalsof Botany 121: 85-105.", "Bellot, S., T. C. Mitchell, and H. Schafer. 2020. Phylogenetic informativeness analyses to clarify past diversification processes in Cucurbitaceae. Scientific Reports 10: 488.", "Bogarin, D., O. A. Perez-Escobar, D. Groenenberg, S. D. Holland, A. K. P. Karremans, E. R. Lemmon, A. R. Lemmon, et al. 2018. Anchored hybrid enrichment generated nuclear, plastid and mitochondrial markers resolve the Lepanthes horrida (Orchidaceae: Pleurothallidinae) species complex. Molecular Phylogenetics and Evolution 129: 27-47.", "Bogarin, D., O.A. Perez-Escobar,A.K.P.Karremans, M.Fernandez, J.Kruizinga, F. Pupulin, E. Smets, and B. Gravendeel. 2019. Phylogenetic comparative methods improve the selection of characters for generic delimitations in a hypediverse Neotropical orchid clade. Scientific Reports 9: 1-17.", "Brandrud, M. K., J. Baar, M. T. Lorenzo, A. Athanasiadis, R. M. Bateman, M. W. Chase,M. Hedren, and O.Paun.2020. Phylogenomic relationshipsof diploids and the origins of allotetraploids in Dactylorhiza (Orchidaceae). Systematic Biology 69: 91-109.", "Brewer,G.E., J.J.Clarkson,O.Maurin,A.R.Zuntini,V.Barber,S.Bellot,N.Biggs, et al. 2019. Factors affecting targeted sequencing of 353 nuclear genes from herbarium specimens spanning the diversity of angiosperms. Frontiers in Plant Science 10: 1102.", "Britton, T., C. L. Anderson, D. Jacquet, S. Lundqvist, and K. Bremer. 2007. Estimating divergence times in large phylogenetic trees. Systematic Biology 56: 741-752.", "Cafasso, D., A.Widmer, and S. Cozzolino. 2005. Chloroplast DNA inheritance in the orchid Anacamptis palustris using single-seedpolymerase chainreaction. Journal of Heredity 96: 66-70.", "Cameron,K.M., M.W.Chase,W.M.Whitten,P.J.Kores, D.C.Jarrell,V.A.Albert, T. Yukawa, et al. 1999. Aphylogenetic analysis of the Orchidaceae: evidence from rbcL nucleotide sequences. American Journal of Botany 86: 208-224.", "Capella-Gutierrez, S., J. M. Silla-Martinez, and T. Gabaldon. 2009. trimAL: a tool for automated alignment trimming in large-scale phylogenetic analyses. Bioinformatics 25: 1972-1973.", "Chang, S.-B.,W.-H. Chen, H.-H.Chen,Y.-M.Fu, and Y.-S. Lin.2000.RFLP and inheritance patterns of chloroplast DNA in intergenic hybrids of Phalaenopsis and Doritis. Botanical Studies 41: 219-223.", "Chase, M. W., K. M. Cameron, J. V. Freudenstein, A. M. Pridgeon, G. Salazar, C. van den Berg, and A. Schuiteman. 2015. An updated classification of Orchidaceae: updated classification of Orchidaceae. Botanical Journal of the Linnean Society 177: 151-174.", "Chase, M. W., D. E. Soltis, R. G. Olmstead, D. Morgan, D. H. Les, B. D. Mishler, M. R. Duvall, et al. 1993. Phylogenetics of seed plants: an analysis of nucleotide sequences from the plastid gene rbc L. Annals of the Missouri Botanical Garden 80: 528-580.", "Chomicki, G., L. P. R. Bidel, F. Ming, M. Coiro, X. Zhang, Y. Wang, Y. Baissac, et al. 2015. The velamen protects photosynthetic orchid roots against UV-B damage, and a large dated phylogeny implies multiple gains and losses of this function during the Cenozoic. New Phytologist 205: 1330-1341.", "Conran, J. G., J. M. Bannister, and D. E. Lee. 2009. Earliest orchid macrofossils: early Miocene Dendrobium and Earina (Orchidaceae:Epidendroideae) from New Zealand.American Journal of Botany 96: 466-474.", "Darwin, C. 1877. On the various contrivances by which british and foreign orchids are fertilised by insects.Appleton and Co., NY, NY, USA.", "De Vienne, D. M., G. Aguileta, and S. Ollier. 2011. Euclidean nature of phylogenetic distance matrices. Systematic Biology 60: 826-832.", "Dearnaley, J. D. W. 2007. Further advances in orchid mycorrhizal research. Mycorrhiza 17: 475-486.", "Dodsworth, S. 2015. Genome skimming for next-generation biodiversity analysis. Trends in Plant Science 20: 525-527.", "Dodsworth, S., M. S. Guignard, M. J. M. Christenhusz, R. S. Cowan, S. Knapp, O. Maurin, M. Struebig, et al. 2018. Potential of herbariomics for studying repetitive DNA in angiosperms. Frontiers in Ecology and Evolution 6: 174.", "Dodsworth, S., L. Pokorny, M. G. Johnson, J. T. Kim, O. Maurin, N. J.Wickett, F. Forest, et al. 2019. Hyb-Seq for flowering plant systematics. Trends in Plant Science 24: 887-891.", "Doyle, J. J., and J. L. Doyle. 1987. A rapid DNA isolation procedure for small quantities of fresh leaf tissue. Phytochemical Bulletin 19: 11-15.", "Dress, A. W., and D. H. Huson. 2004. Constructing splits graphs. IEEE/ACM Transactions on Computational and Biology Bioinformatics 1: 109-115.", "Dressler,R.L.1993.Phylogenyand classificationof the orchidfamily.Dioscorides Press, Portland, OR, USA.", "Edger, P. P., J. C. Hall, A. Harkess, M. Tang, J. Coombs, S. Mohammadin, M. E. Schranz, et al. 2018. Brassicales phylogeny inferred from 72 plastid genes: a reanalysis of the phylogenetic localization of two paleopolyploid events and origin of novel chemical defenses. American Journal of Botany 105: 463-469.", "Eiserhardt, W. L., A. Antonelli, D. J. Bennett, L. R. Botigue, J. G. Burleigh, S. Dodsworth, B. J. Enquist, et al. 2018. A roadmap for global synthesis of the plant tree of life. American Journal of Botany 105: 614-622.", "Feliner, G. N., and J. A. Rosello. 2007. Better the devil you know? Guidelines for insightful utilization of nrDNA ITS in species-level evolutionary studies in plants. Molecular Phyogenetics and Evolution 44: 911-919.", "Fernandez-Mazuecos, M., G. Mellers, B. Vigalondo, L. Saez, P. Vargas, and B. J. Glover. 2018. Resolving recent plant radiations: power and robustness of Genotyping-by-Sequencing.Systematic Biology 67: 250-268.", "Fochi, V., W. Chitarra, A. Kohler, S. Voyron, V. R. Singan, E. A. Lindquist, K. W. Barry, et al. 2017. Fungal and plant gene expression in the Tulasnella calospora-Serapiasvomeracea symbiosis providesclues about nitrogenpathways in orchid mycorrhizas. New Phytologist 213: 365-379.", "Freudenstein, J. V., and M. W. Chase. 2015. Phylogenetic relationships in Epidendroideae (Orchidaceae), one of the great flowering plant radiations: progressive specializationand diversification.Annalsof Botany 115: 665-681.", "Galili, T. 2015. dendextend: An Rpackage for visualizing, adjusting and comparing trees of hierarchical clustering. Bioinformatics 31: 3718-3720.", "Givnish,T.J.,D.Spalink,M.Ames,S.P.Lyon,S.J.Hunter,A.Zuluaga,A.Doucette, etal. 2016.Orchid historical biogeography, diversification,Antarctica and the paradox of orchid dispersal. Journal of Biogeography 43: 1905-1916.", "Givnish,T.J., D.Spalink,M.Ames, S.P.Lyon,S. J.Hunter,A.Zuluaga,W.J.D.Iles, et al. 2015. Orchid phylogenomics and multiple drivers of their extraordinary diversification. Proceedings of the Royal Society, B, Biological Sciences 282: 1553.", "Givnish, T. J., A. Zuluaga, D. Spalink, M. Gomez, V. K. Lam, J. M. S. Saarela, Ch Saas, et al. 2018. Monocot plastid phylogenomics, timeline, net rates of species diversification, the power of multi-gene analyses, and functional model for the origin of monocots. American Journal of Botany 105: 1888-1910.", "Goncalves,D.J.P., R.K.Jansen, T.A. Ruhlman,and J.R.Mandel.2020.Underthe rug: abandoning persistent misconceptions that obfuscate organelle variation.Molecular Phylogenetics and Evolution 151: 106903.", "Goncalves, D. J. P., B. B. Simpson, E. M. Ortiz, G. H. Shimizu, and R. K. Jansen. 2019. Incongruence between gene trees and species trees and phylogenetic signal variation in plastid genes. Molecular Phylogenetics and Evolution 138: 219-232.", "Gorniak, M., O. Paun, and M. W. Chase. 2010. Phylogenetic relationships within Orchidaceae based on a low-copy nuclear coding gene, Xdh: congruence with organellar and nuclear ribosomal DNA results. Molecular Phylogenetics and Evolution 56: 784-795.", "Grace, O., O. A.Perez-Escobar, E. J. Lucas, M.Vorontsova, G. P. Lewis, B.Walker, et al. 2021. Botanical monograph in the Anthropocene. Trends in Plant Science 26: 433-441.", "Guo, X., J.Liu,G.Hao,L.Zhang,K.Mao,X.Wang,D.Zhang,etal.2017.Plastome phylogeny and early diversification of Brassicaceae. BMC Genomics 18: 176.", "Henriquez, C. L., T. Arias, J. C. Pires, T. B. Croat, and B. A. Schaal. 2014. Phylogenomics of the plant family Araceae. Molecular Phylogenetics and Evolution 75: 91-102.", "Hilu, K. W., T. Borsch, K. Muller, D. E. Soltis, P. S. Soltis, V. Savolainen, M. W. Chase, et al.2003.Angiosperm phylogeny based on ma tK sequence information.American Journal of Botany 90: 1758-1776.", "Huson, D. H. 1998. SplitsTree: analyzing and visualizing evolutionary data. Bioinformatics 14: 68-73.", "Jersakova, J., and T. Malinova. 2004. Spatial aspects of seed dispersal and seedling recruitment in orchids. New Phytologist 176: 237-241.", "Johnson, M. G., E. M. Gardner,Y. Liu, R. Medina, B. Goffinet,A. J. Shaw, N. J. C. Zerega, and N. J. Wickett. 2016. HybPiper: extracting coding sequence and introns for phylogenetics from high-throughput sequencing reads using target enrichment. Applications in Plant Sciences 4: 1600016.", "Johnson, M., L. Pokorny, S. Dodsworth, L. Botigue, S. Cowan, A. Devault, W. L. Eiserhardt, et al. 2019. A universal probe set for targeted sequencing of 353 nuclear genes from any flowering plant designedusing k -medoids clustering. Systematic Biology 7: 594-606.", "Joly, S. 2011. JML: testing hybridizatin from species trees. Molecular Ecology Resources 12: 179-184.", "Junier, T., and E. M. Zdobnov. 2010. The Newick utilities: high-throughput phylogenetic tree processing in the UNIX shell. Bioinformatics 26: 1669-1670.", "Katoh, K., and D. M. Standley. 2013. MAFFT: multiple sequence alignment software version 7: improvements in performance and usability. Molecular Biology and Evolution 30: 772-780.", "Kim,Y. K., S. Jo, S. H. Cheon, M. J. Joo, J. R. Hong, M.Kwak, and K. J. Kim. 2020. Plastome evolution and phylogeny of Orchidaceae, with 24 new sequences. Frontiers in Plant Science 11: 22.", "Kosakovsky Pond, S. L., S. D. W. Frost, and S. V. Muse. 2005. HyPhy: hypothesis testing using phylogenies. Bioinformatics 21: 676-679.", "Li, H., and R. Durbin. 2009. Fast and accurate short read alignment with Burrows-Wheeler transform.Bioinformatics 25: 1754-1760.", "Li, H. T., T. S. Yi, L. M. Gao, P. F. Ma, T. Zhang, J. B. Yang, M. A. Gitzendanner, et al. 2019a. Origin of angiosperms and the puzzle of the Jurassic gap. Nature Plants 5: 461-470.", "Li, Y.-X., Z.-H. Li, A. Schuiteman, M. W. Chase, J.-W. Li, W.-C. Huang, A. Hidayat, et al. 2019b. Phylogenomics of Orchidaceae based on plastid and mitochondrial genomes. Molecular Phylogenetics and Evolution 139: 106540.", "Lopez-Giraldez, F., and J. P. Townsend. 2011. PhyDesign: an online application for profiling phylogenetic informativeness. BMC Evolutionary Biology 11: 152.", "Martins, A., T. Bochorny, O.A. Perez-Escobar, G. Chomicki, S. Monteiro, and E. Smidt. 2018. From tree tops to the ground: reversals to terrestrial habit in Galeandra orchids (Epidendroideae: Catasetinae). Molecular Phylogenetics and Evolution 127: 952-960.", "Matzke, N.2013a.BioGeoBEARS:BioGeography with Bayesian (and Likelihood) Evolutionary Analysis in R Scripts. University of California, Berkeley, Berkeley, CA, USA.", "Matzke, N. J. 2013b. Probabilistic historical biogeography: new models for founder-event speciation, imperfect detection, and fossil allow improved accuracy and model-testing. Frontiers of Biogeography 5: 243-248.", "Morales-Briones, D. F., A. Liston, and D. C. Tank. 2018a. Phylogenomic analyses reveal a deep history of hybridization and polyploidy in the Neotropical genus Lachemilla (Rosaceae). New Phytologist 218: 1668-1684.", "Morales-Briones, D.F., K. Romoleroux,F.Kolar, and D.C.Tank.2018b.Phylogeny and evolution of the neotropical radiation of Lachemilla (Rosaceae): uncovering a history of reticulate evolutionand implications for infrageneric classification. Systematic Botany 43: 17-34.", "Morales-Linares, J., J. G. Garcia-Franco, A. Flores-Palacios, J. E. Valenzuela- Gonzalez, M. Mata-Rosas, and C. Diaz-Castelazo.2018. Orchid seed removal by ants in Neotropical ant-gardens. Plant Biology 20: 525-530.", "Nauheimer, L., R. J. Schley, M. A. Clements, C. Micheneau, and K. Nargar. 2018. Australasian orchid biogeography at continental scale: molecular phylogenetic insights from the Sun Orchids (Thelymitra, Orchidaceae). Molecular Phylogenetics and Evolution 127: 304-319.", "Neubig, K. M., W. M. Whitten, N. H. Williams, M. A. Blanco, L. Endara, J. G. Burleigh, K. Silvera, et al. 2012. Generic recircumscriptions of Oncidiinae (Orchidaceae: Cymbidieae) based on maximum likelihood analysis of combined DNA datasets. Botanical Journal of the Linnean Society 168: 117-146.", "Neyland, R., and L. E. Urbatsch. 1996. Phylogeny of subfamily Epidendroideae (Orchidaceae) inferred from ndhF chloroplast gene sequences. American Journal of Botany 83: 1195-1206.", "Nute, M., J. Chou, E. K. Molloy, and T. Warnow. 2018. The performance of coalescent-based species tree estimation methods under models of missing data.BMC Genomics 19: 286.", "Paradis, E., J. Claude, and K. Strimmer. 2004.APE:Analyses of phylogenetics and evolution in R language. Bioinformatics 20: 289-290.", "Parks, M., R. Cronn, and A. Liston. 2009. Increasing phylogenetic resolution at low taxonomic levels using massively parallel sequencing of chloroplast genomes. BMC Biology 7: 84.", "Perez-Escobar, O. A. 2016. Molecular phylogenetics, evolution of sexual systems and historical biogeography of Darwin's favorite orchids (Catasetinae) and Swan orchids (Cycnoches Lindl.). Ph.D. dissertation, Ludwig-Maximilians Universitat, Munich, Germany.", "Perez-Escobar, O.A., J.A.Balbuena, and M.Gottschling. 2016. Rumblingorchids: how to assess divergent evolution between chloroplast endosymbionts and the nuclear host. Systematic Biology 65: 51-65.", "Perez-Escobar, O. A., D. Bogarin, R. Schley, R. M. Bateman, G. Gerlach, D. Harpke, J. Brassac, et al. 2020. Resolving relationships in an exceedingly young Neotropical orchid lineage using Genotyping-by-sequencing data. Molecular Phylogenetics and Evolution 144: 106672.", "Perez-Escobar,O.A., G.Chomicki,F.L.Condamine,A.P.Karremans,D.Bogarin, N. J. Matzke, D. Silvestro, and A. Antonelli. 2017a. Recent origin and rapid speciation of Neotropical orchids in the world's richest plant biodiversity hotspot. New Phytologist 215: 891-905.", "Perez-Escobar,O.A., G.Chomicki,F.L.Condamine, J.M.deVos,A.C.Martins,E. C. Smidt, B. Klitgard, et al. 2017b. Multiple geographical origins of environmental sex determination enhanced the diversification of Darwin's favourite orchids. Scientific Reports 7: 12878.", "Perez-Escobar, O. A., S. Bellot, N. A. S. Przelomska, J. M. Flowers, M. Nesbitt, P. Ryan, R. M. Gutaker, et al. 2021. Molecular clocks and archaeogenomics of a Late Period Egyptian date palm leaf reveal introgression from wild relatives and add timestamps on the domestication. Molecular Biology and Evolution: in press.", "Ramirez, S. R., T. Eltz, M. K. Fujiwara, G. Gerlach, B. Goldman-Huertas, N. D. Tsutsui, and N. E. Pierce. 2011. Asynchronous diversification in a specialized plant-pollinator mutualism.Science 333: 1742-1746.", "Rasmussen, F. N. 2015. Trophic relationships in orchid mycorrhiza-diversity and implications for conservation and implications for conservation. Lankesteriana 7: 334-341.", "Renner, S. S., S. Wu, O. A. Perez-Escobar, M. V. Silber, Z. Fei, and G. Chomicki. 2021. Achromosome-level genome of a Kordofan melon illuminates the origin of domesticated watermelons. Proceedings of the National Academy of Sciences, USA 118: e2101486118.", "Rieseberg, L. H., J.Whitton, and C. R. Linder. 1996. Molecular marker incongruence in plant hybridzones and phylogenetic trees. Acta Botanica Neerlandica 45: 243-262.", "Ross, T. G., C. F. Barrett, M. Soto Gomez, V. K. Y. Lam, C. L. Henriquez, D. H. Les, J. I. Davis, et al. 2016. Plastid phylogenomics and molecular evolution of Alismatales. Cladistics 32: 160-178.", "Rutherford, S., M. Rossetto, J. G. Bragg, H. McPherson, D. Benson, S. P. Bonser, and P. G. Wilson. 2018. Speciation in the presence of gene flow: population genomics of closely related and diverging Eucalyptus species. Heredity 121: 1-16.", "Salazar, G. A., M. W. Chase, M. A. Soto Arenas, and M. Ingrouille. 2003. Phylogenetics of Cranichideae with emphasis on Spiranthinae (Orchidaceae, Orchidoideae):evidence from plastidand nuclear DNA sequences.American Journal of Botany 90: 777-795.", "Sayyari, E., and S. Mirarab. 2016. Fast coalescent-based computation of local banch supportfromquartetfrequencies.MolecularBiologyandEvolution33:1654-1668.", "Schlechter, R. 1926. Das System der Orchidaceen. Notizblatt des Koniglischen botanischen Gartens und Museums zu Berlin 9: 563-591.", "Schley,R. J., M.de la Estrella, O.A.Perez-Escobar,A.Bruneau, T. Barraclough, F. Forest, and B. Klitgaard. 2018. Is Amazona a 'museum' for Neotropical trees? The evolution of the Brownea clade (Detarioideae, Leguminosae). Molecular Phylogenetics and Evolution 126: 279-292.", "Schley, R. J., R. T. Pennington, O. A. Perez-Escobar, A. J. Helmstetter, M. de la Estrella, I. Larridon, I. A. B. Sabino Kikuchi, et al. 2020. Introgression across evolutionary scales suggests reticulation contribu

The date palm, Phoenix dactylifera, has been a cornerstone of Middle Eastern and North African agriculture for millennia. It was first domesticated in the Persian Gulf, and its evolution appears to have been influenced by gene flow from two wild relatives, P. theophrasti, currently restricted to Crete and Turkey, and P. sylvestris, widespread from Bangladesh to the West Himalayas. Genomes of ancient date palm seeds show that gene flow from P. theophrasti to P. dactylifera may have occurred by ∼2,200 years ago, but traces of P. sylvestris could not be detected. We here integrate archeogenomics of a ∼2,100-year-old P. dactylifera leaf from Saqqara (Egypt), molecular-clock dating, and coalescence approaches with population genomic tests, to probe the hybridization between the date palm and its two closest relatives and provide minimum and maximum timestamps for its reticulated evolution. The Saqqara date palm shares a close genetic affinity with North African date palm populations, and we find clear genomic admixture from both P. theophrasti, and P. sylvestris, indicating that both had contributed to the date palm genome by 2,100 years ago. Molecular-clocks placed the divergence of P. theophrasti from P. dactylifera/P. sylvestris and that of P. dactylifera from P. sylvestris in the Upper Miocene, but strongly supported, conflicting topologies point to older gene flow between P. theophrasti and P. dactylifera, and P. sylvestris and P. dactylifera. Our work highlights the ancient hybrid origin of the date palms, and prompts the investigation of the functional significance of genetic material introgressed from both close relatives, which in turn could prove useful for modern date palm breeding., Molecular Biology and Evolution, 38 (10), ISSN:0737-4038, ISSN:1537-1719

AimPhenotypes which evolved for dispersal over ecological timescales may lead to significant macroevolutionary consequences, such as infrequent long-distance dispersal and diversification in novel biomes. We aimed to reconstruct the phylogenetic history of Pterocarpus (Leguminosae/ Fabaceae) to assess whether seed dispersal phenotypes and biome switching explain the current biogeographical patterns of this group.LocationPantropicalTaxonThe Pterocarpus clade, particularly Pterocarpus (Leguminosae/Fabaceae)MethodsWe sequenced ~300 nuclear loci captured using Angiosperms-353, a genomic ‘bait set’ for flowering plants, from which we generated a time-calibrated phylogenomic tree. To corroborate this, we also generated a time-calibrated phylogenetic tree from data-mined Sanger-sequencing data. We then collated distribution data and fruit dispersal morphology traits to compare trait-dependent and trait-independent biogeographical models, allowing us to assess whether dispersal traits influenced the spatio-temporal evolution of Pterocarpus. Finally, using the results of these model tests, we estimated the ancestral ranges and biomes of Pterocarpus species to better understand their biogeographical history, and assessed the degree and direction of biome switching over the course of Pterocarpus’ diversification history.ResultsWe recovered well-supported phylogenetic relationships within Pterocarpus, within which there were two subclades – one Neotropical and the other Palaeotropical. Our divergence date estimates suggested that Pterocarpus largely diversified from around 12 Ma, during the Miocene.Trait-dependent biogeographical models were rejected for both range and biome evolution within Pterocarpus, but models parameterising dispersal were supported. Pterocarpus’ ancestral node shared a range across the new-world and old-world tropics, followed by divergence into two clades, one palaeotropical and one neotropical. Biome switching occurred most frequently into rainforest and grassland.Main conclusionsOverall, our analyses suggest that Pterocarpus underwent infrequent cross-continental dispersal and establishment into novel biomes. While this was minimally impacted by fruit dispersal syndromes, biome switching precipitated by long-distance dispersal and environmental change have played an important role in diversification within Pterocarpus since the Miocene.

Well-supported phylogenies are a prerequisite for the study of the evolution and diversity of life on earth. The subfamily Calamoideae accounts for more than one fifth of the palm family (Arecaceae), occurs in tropical rainforests across the world, and supports a billion-dollar industry in rattan products. It contains ca. 550 species in 17 genera, 10 subtribes and three tribes, but their phylogenetic relationships remain insufficiently understood. Here, we sequenced almost one thousand nuclear genomic regions for 75 systematically selected Calamoideae, representing the taxonomic diversity within all calamoid genera. Our phylogenomic analyses resolved a maximally supported phylogenetic backbone for the Calamoideae, including several higher-level relationships not previously inferred. In-depth analysis revealed low gene tree conflict for the backbone but complex deep evolutionary histories within several subtribes. Overall, our phylogenomic framework sheds new light on the evolution of palms and provides a robust foundation for future comparative studies, such as taxonomy, systematics, biogeography, and macroevolutionary research.

The date palm (Phoenix dactylifera) has been a cornerstone of Middle Eastern and North African agriculture for millennia. It is presumed that date palms were first domesticated in the Persian Gulf and subsequently introduced into North Africa, where their evolution in the latter region appears to have been influenced by gene flow from the wild relative P. theophrasti, which is restricted to Crete and Turkey. However, the timing of gene flow from P. theophrasti to P. dactylifera remains unknown due to the limited archaeobotanical evidence of P. theophrasti and their exclusion from population genomic studies.We addressed this issue by investigating the relatedness and ancestry of a ~2,100-year-old P. dactylifera leaf from Saqqara (Egypt), combining genome sequencing of this ancient specimen with a broad sample of date palm cultivars and closely related species.The ancient Saqqara date palm shares close genetic ancestry with North African date palm populations. We find clear genomic admixture between the Saqqara date palm, P. theophrasti and the closest known relative P. sylvestris.Our study highlights that gene flow from P. theophrasti and P. sylvestris to North African date palms had already occurred at least ~2,100 years ago, providing a minimum timestamp for hybridisation between species.

Premise of the studyEvolutionary relationships in the species-rich Orchidaceae have historically relied on organellar DNA sequences and limited taxon sampling. Previous studies provided a robust plastid-maternal phylogenetic framework, from which multiple hypotheses on the drivers of orchid diversification have been derived. However, the extent to which the maternal evolutionary history of orchids is congruent with that of the nuclear genome has remained uninvestigated.MethodsWe inferred phylogenetic relationships from 294 low-copy nuclear genes sequenced/obtained using the Angiosperms353 universal probe set from 75 species representing 69 genera, 16 tribes and 24 subtribes. To test for topological incongruence between nuclear and plastid genomes, we constructed a tree from 78 plastid genes, representing 117 genera, 18 tribes and 28 subtribes and compared them using a co-phylogenetic approach. The phylogenetic informativeness and support of the Angiosperms353 loci were compared with those of the 78 plastid genes.Key ResultsPhylogenetic inferences of nuclear datasets produced highly congruent and robustly supported orchid relationships. Comparisons of nuclear gene trees and plastid gene trees using the latest co-phylogenetic tools revealed strongly supported phylogenetic incongruence in both shallow and deep time. Phylogenetic informativeness analyses showed that the Angiosperms353 genes were in general more informative than most plastid genes.ConclusionsOur study provides the first robust nuclear phylogenomic framework for Orchidaceae plus an assessment of intragenomic nuclear discordance, plastid-nuclear tree incongruence, and phylogenetic informativeness across the family. Our results also demonstrate what has long been known but rarely documented: nuclear and plastid phylogenetic trees are not fully congruent and therefore should not be considered interchangeable.

Poor morphological and molecular differentiation in recently diversified lineages is a widespread phenomenon in plants. Phylogenetic relationships within such species complexes are often difficult to resolve because of the low variability in traditional molecular loci. Furthermore, biological phenomena responsible for topological incongruence such as Incomplete Lineage Sorting (ILS) and hybridisation complicate the resolution of phylogenetic relationships among closely related taxa. In this study, we employ a Genotyping-by-sequencing (GBS) approach to disentangle evolutionary relationships within a species complex belonging to the Neotropical orchid genus Cycnoches. This complex includes seven taxa distributed through Central America and the Colombian Chocó, and is nested within a clade estimated to have first diversified in the early Quaternary. Previous phylogenies inferred from few loci failed to provide support for internal relationships within the complex. Our Neighbour-net and coalescent-based analyses inferred from ca. 13,000 GBS loci obtained from 31 individuals belonging to six of the seven traditionally accepted Cycnoches taxa provided a robust phylogeny for this group. The genus Cycnoches includes three main clades that are further supported by morphological traits and geographic distributions. Similarly, a topology reconstructed through maximum likelihood (ML) inference of concatenated GBS loci produced results that are comparable with those reconstructed through coalescence and network-based methods. Our comparative phylogenetic informativeness analyses suggest that the low support evident in the ML phylogeny might be attributed to the abundance of uninformative GBS loci, which can account for up to 50% of the total number of loci recovered. The phylogenomic framework provided here, as well as morphological evidence and geographical patterns, suggest that the six entities previously thought to be different species or subspecies might actually represent only three distinct segregates. We further discuss the limited phylogenetic informativeness found in our GBS approach and its utility to disentangle relationships within recent and rapidly evolving species complexes. Our study is the first to demonstrate the utility of GBS data to reconstruct relationships within young (~2 Ma) Neotropical plant clades, opening new avenues for studies of species complexes that populate the species-rich orchid family UCR::Vicerrectoría de Investigación::Unidades de Investigación::Ciencias Agroalimentarias::Jardín Botánico Lankester (JBL)

Poor morphological and molecular differentiation in recently diversified lineages is a widespread phenomenon in plants. Phylogenetic relationships within such species complexes are often difficult to resolve because of the low variability in traditional molecular loci, as well as various other biological phenomena responsible for topological incongruence such as ILS and hybridization. In this study, we employ a Genotyping-by-sequencing (GBS) approach to disentangle evolutionary relationships within a species complex belonging to the Neotropical orchid genus Cycnoches. The complex includes seven taxa distributed in Central America and the adjacent Chocó biogeographic region, nested within a clade estimated to have first diversified in the early Quaternary. Previous phylogenies inferred from a handful of loci failed to provide support for internal relationships within the complex. Our Neighbor-net and coalescent-based analyses inferred from ca. 13,000 GBS loci obtained from 31 individuals belonging to six of the seven traditionally accepted Cycnoches species provided a robustly supported network. The resulting three main clades are corroborated by morphological traits and geographical distributions. Similarly, Maximum Likelihood (ML) inferences of concatenated GBS-loci produced results comparable with those derived from coalescence and network-based methods, albeit always with poor statistical support. The low support evident in the ML phylogeny might be attributed to the abundance of uninformative GBS loci, which can account for up to 50% of the total number of loci recovered. The phylogenomic framework provided here, as well as morphological evidence and geographical patterns, suggest that the six entities previously thought to be different species might actually represent only three distinct segregates. Our study is the first to demonstrate the utility of GBS data in phylogenomic research of a very young Neotropical plant clade (~2 Ma), and it paves the way for the study of the many other species complexes that populate the species-rich orchid family.

The flora of the Neotropics is unmatched in its diversity, however the mechanisms by which diversity has accumulated are debated and largely unclear. The Brownea clade (Leguminosae) is a characteristic component of the Neotropical flora, and the species within it are diverse in their floral morphology, attracting a wide variety of pollinators. This investigation aimed to estimate species divergence times and infer relationships within the group, in order to test whether the Brownea clade followed the 'cradle' or 'museum' model of diversification, i.e. whether species evolved rapidly over a short time period, or gradually over many millions of years. We also aimed to trace the spatio-temporal evolution of the clade by estimating ancestral biogeographical patterns in the group. We used BEAST to build a dated phylogeny of 73 Brownea clade species using three molecular markers (ITS, trnK and psbA-trnH), resulting in well-resolved phylogenetic relationships within the clade, as well as robust divergence time estimates from which we inferred diversification rates and ancestral biogeography. Our analyses revealed an Eocene origin for the group, after which the majority of diversification happened in Amazonia during the Miocene, most likely concurrent with climatic and geological changes caused by the rise of the Andes. We found no shifts in diversification rate over time, suggesting a gradual accumulation of lineages with low extinction rates. These results may help to understand why Amazonia is host to the highest diversity of tree species on Earth.

Australia harbours a rich and highly endemic orchid flora, with c. 90% of species endemic to the country. Despite that, the biogeographic history of Australasian orchid lineages is only poorly understood. Here we examined evolutionary relationships and the spatio-temporal evolution of the sun orchids (Thelymitra, 119 species), which display disjunct distribution patterns frequently found in Australasian orchid lineages. Phylogenetic analyses were conducted based on one nuclear (ITS) and three plastid markers (matK, psbJ-petA, ycf1) using Maximum Likelihood and Bayesian inference. Divergence time estimations were carried out with a relaxed molecular clock in a Bayesian framework. Ancestral ranges were estimated using the dispersal-extinction-cladogenesis model and an area coding based on major disjunctions. The phylogenetic analyses clarified intergeneric relationships within Thelymitrinae, with Epiblema being sister to Thelymitra plus Calochilus, both of which were well-supported. Within Thelymitra, eight major and several minor clades were retrieved in the nuclear and plastid phylogenetic reconstructions. Five major clades corresponded to species complexes previously recognized based on morphological characters, whereas other previously recognized species groups were found to be paraphyletic. Conflicting signals between the nuclear and plastid phylogenetic reconstructions provided support for hybridization and plastid capture events both in the deeper evolutionary history of the genus and more recently. Divergence time estimation placed the origin of Thelymitra in the late Miocene (c. 10.8 Ma) and the origin of the majority of the main clades within Thelymitra during the late Pliocene and early Pleistocene, with the majority of extant species arising during the Pleistocene. Ancestral range reconstruction revealed that the early diversification of the genus in the late Miocene and Pliocene took place predominantly in southwest Australia, where most species with highly restricted distributional ranges occur. Several long-distance dispersal events eastwards across the Nullarbor Plain were inferred, recurrently resulting in lineage divergence within the genus. The predominant eastwards direction of long-distance dispersal events in Thelymitra highlights the importance of the prevailing westerly winds in the Southern Hemisphere for the present-day distribution of the genus, giving rise to the Thelymitra floras of Tasmania, New Zealand and New Caledonia, which were inferred to be of comparatively recent origin.

Premise of research. The Neotropical endemic Macrolobium is one of the most species-rich genera (ca. 75 species) within subfamily Detarioideae (Fabaceae, alternatively Leguminosae). Two sections distinguished by floral morphology have been recognized in the past. Although morphologically diverse, species within the genus share several characters, including a single well-developed petal in adaxial position. However, previous analyses based on plastid markers have suggested that the genus is not monophyletic. We produce the most densely sampled molecular phylogeny of Macrolobium and test the monophyly of the genus and the two sections. Methodology. We analyzed nucleotide sequence data from the nuclear ribosomal internal transcribed spacer (ITS) and plastid (matK, trnG) genomes using Bayesian and maximum likelihood analyses. Pivotal results. The combined analysis retains Macrolobium as a monophyletic genus, with two well-supported subclades corresponding to the two recognized sections. Macrolobium pendulum is the only species placed in a section different from its taxonomic treatment. The relationships recovered with the plastid markers differ slightly from the combined and ITS analyses, but without significant support. Conclusions. Macrolobium is shown to be a monophyletic genus and to contain two well-supported and morphologically defined sections with differing Amazonian and Andean/Central American distributions corresponding to the Gentry pattern. Species are also found to group partly according to habitat preferences and leaf morphology. Both sections contain groups of multijugate and unijugate species, and there appear to have been multiple shifts of this character.