Abstract
We present an updated review of the phylogenetic and evolutionary studies conducted on the model genus Brachypodium. The genus, which contains approximately 20 globally distributed taxa (17 species, 1 variety, and 2 undescribed cytotypes) shows an intermediate evolutionary placement within the grass temperate pooid clade, being closer to the basal than to the recent Pooideae lineages. Our comprehensive molecular phylogenetic survey of all the currently known Brachypodium lineages illustrates a complex reticulate scenario of recently evolved diploid and allopolyploid lineages. Haplotypic statistical parsimony networks, multilabelled (multigenic) Minimum Evolution gene tree discordances, and Bayesian dating analysis have provided a testable hypothesis for the reconstruction of the Brachypodium species tree and for the estimation of its nodal divergence times. Our results support the early splits of the annual and short-rhizomatose lineages (B. stacei, B. mexicanum, B. distachyon) in the Holarctic region during the early-Middle Miocene (and B. hybridum in the Pleistocene), and a profusion of rapid splits for the perennial lineages since the late Miocene to the Pleistocene in the Mediterranean and Eurasian regions, with sporadic colonizations of more remote areas. Several perennial allopolyploid species (B. boissieri, B. retusum, B. phoenicoides, B. rupestre 4x, B. pinnatum 4x) showed homeologous copies from both ancestral and recent genome donors. More in-depth studies of the species of the B. distachyon complex have demonstrated the polyphyletic origin of the allotetraploid B. hybridum from bidirectional crosses of its diploid B. stacei and B. distachyon parents. Our niche modeling analysis has also detected distinct adaptations to different ecological tolerances in the diploids and evidence of niche conservatism for B. hybridum and each of its parents in their native Mediterranean region. Future perspectives include ongoing comparative genomics, phylogenomic and genotype-based phylogeographic studies of Brachypodium.
Access this chapter
Tax calculation will be finalised at checkout
Purchases are for personal use only
References
Bakker EG, Montgomery B, Nguyen T, Eide K, Chang J, Mockler TC, et al. Strong population structure characterizes weediness gene evolution in the invasive grass species Brachypodium distachyon. Mol Ecol. 2009;18:2588–601.
Betekhtin A, Jenkins G, Hasterok R. Reconstructing the evolution of Brachypodium genomes using comparative chromosome painting. PLoS One. 2014;9(12):e115108.
Bouchenak-Khelladi Y, Salamin N, Savolainen V, Forest V, Van der Bank M, Chase MW, et al. Large multi-gene phylogenetic trees of the grasses (Poaceae): progress towards complete tribal and generic level sampling. Mol Phylogenet Evol. 2008;47:488–505.
Bouchenak-Khelladi Y, Verboom GA, Savolainen V, Hodkinson TR. Biogeography of the grasses (Poaceae): a phylogenetic approach to reveal evolutionary history in geographical space and geological time. Bot J Linn Soc. 2010;162:543–57.
Cai D, Rodriguez F, Teng Y, Ane C, Bonierbale M, Mueller LA, et al. Single copy nuclear gene analysis of polyploidy in wildpotatoes (Solanum section Petota). BMC Evol Biol. 2012;12:70.
Catalán P, Olmstead RG. Phylogenetic reconstruction of the genus Brachypodium P. Beauv. (Poaceae) from combined sequences of chloroplast ndhF gene and nuclear ITS. Plant Syst Evol. 2000;220:1–19.
Catalán P, Shi Y, Amstrong L, Draper J, Stace CA. Molecular phylogeny of the grass genus Brachypodium P. Beauv based on RFLP and RAPD analysis. Bot J Linn Soc. 1995;177:263–80.
Catalán P, Kellogg EA, Olmstead RG. Phylogeny of Poaceae subfamily Pooideae based on chloroplast ndhF gene sequencing. Mol Phylogenet Evol. 1997;8:1–18.
Catalán P, Müller J, Hasterok R, Jenkins G, Mur LA, Langdon T, et al. Evolution and taxonomic split of the model grass Brachypodium distachyon. Ann Bot. 2012;109:385–405.
Catalán P, Chalhoub B, Chochois V, Garvin DF, Hasterok R, et al. Update on the genomics and basic biology of Brachypodium International Brachypodium Initiative (IBI). Trends in Plant Science. 2014;19:414–8.
Clayton WD, Vorontsoba M, Harman KT, Williamson H. World checklist of Poaceae. Kew: Royal Botanic Gardens. 2015. http://www.kew.org/data/grasses-db.
Davis JI, Soreng RJ. A preliminary phylogenetic analysis of the grass subfamily Pooideae (Poaceae), with attention to structural features of the plastid and nuclear genomes, including an intron loss in GBSSI. Aliso. 2007;23:335–48.
Diaz-Pérez A, Sharifi-Tehrani M, Inda LA, Catalán P. Polyphyly, gene-duplication and extensive allopolyploidy framed the evolution of the ephemeral Vulpia grasses and other fine-leaved Loliinae (Poaceae). Mol Phylogenet Evol. 2014;79:92–105.
Garvin DF, Gu YQ, Hasterok R, Hazen SP, Jenkins G, Mockler TC, et al. Development of genetic and genomic research resources for Brachypodium distachyon, a new model system for grass crop research. Crop Sci. 2008;48:69–84.
Giraldo P, Rodriguez-Quijano M, Vazquez JF, Carillo JM, Benavente E. Validation of microsatellite markers for cytotype discrimination in the model grass Brachypodium. Genome. 2012;55:1–5.
Gómez C, Espadaler X. Myrmecochorous dispersal distances: a world survey. J Biogeogr. 1998;25:573–80.
Gordon SP, Priest H, Marais DLD, Schackwitz W, Figueroa M, Martin J, et al. Genome diversity in Brachypodium distachyon: deep sequencing of highly diverse inbred lines. Plant J. 2014;79:361–74.
GPWG. The Grass Phylogeny Working Group. Phylogeny and subfamilial classification of the grasses (Poaceae). Ann Mo Bot Gard. 2001;88:373–457.
Hammami R, Jouve N, Cuadrado A, Soler C, Gonzalez JM. Prolamin storage proteins and alloploidy in wild populations of the small grass Brachypodium distachyon (L.) P. Beauv. Plant Syst Evol. 2011;297:99–111.
Hamrick JL, Godt MJW. Effects of life history traits on genetic diversity in plant species. Philos Trans R Soc Lond B Biol Sci. 1996;351:1291–8.
International Brachypodium Initiative (IBI). Genome sequencing and analysis of the model grass Brachypodium distachyon. Nature. 2010;463:763–8.
Idziak D, Betekhtin A, Wolny E, Lesniewska K, Wright J, Febrer M, et al. Painting the chromosomes of Brachypodium: current status and future prospects. Chromosoma. 2011;120:469–79.
Idziak D, Hazuka I, Poliwczak B, Wiszynska A, Wolny E, Hasterok R. Insight into the karyotype evolution of Brachypodium species using comparative chromosome barcoding. PLoS One. 2014;9:e93503.
Jaaska V. Isozyme variation and differentiation of morphologically cryptic species in the Brachypodium distachyon complex. Biochem Syst Ecol. 2014;56:185–90.
Jacques-Félix H. Les Graminées d’Afrique Tropicale. Paris: Institut des Recherches Agronomiques Tropicales et des Cultures Vivrières; 1962. p. 168–78.
Jenkins G, Hasterok R, Draper J. Building the molecular infrastructure of a new model grass. In: Zwierzykowski Z, Surma M, Kachlicki P, editors. Applications of novel cytogenetic and molecular techniques in genetics and breeding of the Grasses. Poznan: Institute of Plant Genetics PAS; 2003. p. 77–84.
Jones G, Sagitov S, Oxelman B. Statistical inference of allopolyploid species networks in the presence of incomplete lineage sorting. Syst Biol. 2013;62:1–12.
Khan MA. Biosystematic studies in Brachypodium (Poaceae). PhD thesis. University of Leicester; 1984.
Khan MA. Seed-protein electrophoretic pattern in Brachypodium P. Beauv species. Ann Bot. 1992;70:61–8.
Khan MA, Stace CA. Breeding relationships in the genus Brachypodium (Poaceae: Pooideae). Nord J Bot. 1999;19:257–69.
López-Alvarez D, López-Herranz ML, Betekhtin A, Catalan P. A DNA barcoding method to discriminate between the model plant Brachypodium distachyon and its close relatives B. stacei and B. hybridum (Poaceae). PLoS One. 2012;7(12):e51058.
López-Alvarez D, Manzaneda AJ, Rey PJ, Giraldo P, Benavente E, Allainguillaume J, et al. Environmental niche variation and evolutionary diversification of the Brachypodium distachyon grass complex species in their native circum-Mediterranean range. Am J Bot. 2015;102:1–16.
Manzaneda AJ, Rey PJ, Bastida JM, Weiss-Lehman C, Raskin E, Mitchell-Olds T. Environmental aridity is associated with cytotype segregation and polyploidy occurrence in Brachypodium distachyon (Poaceae). New Phytol. 2012;193:797–805.
Marcussen T, Sandve SR, Heier L, Spannagl M, Pfeifer M, IWGSC, et al. Ancient hybridizations among the ancestral genomes of bread wheat. Science. 2014;345(6194). doi:10.1126/science.1250092.
Marcussen T, Heier L, Brysting AK, Oxelman B, Jakobsen KS. From gene trees to a dated allopolyploid network: insights from the Angiosperm Genus Viola (Violaceae). Syst Biol. 2015;64:84–101.
Meimberg H, Rice KJ, Milan NF, Njoku CC, McKay JK. Multiple origins promote the ecological amplitude of allopolyploid Aegilops (Poaceae). Am J Bot. 2009;96:1262–73.
Minaya M, Pimentel M, Mason-Gamer R, Catalan P. Distribution and evolutionary dynamics of Stowaway Miniature Inverted repeat Transposable Elements (MITEs) in grasses. Mol Phylogenet Evol. 2013;68:106–18.
Minaya M, Díaz-Pérez AJ, Mason-Gamer R, Pimentel M, Catalán P. Evolution of the beta-amylase gene in the temperate grasses: non-purifying selection, recombination, semiparalogy, homeology and phylogenetic signal. Mol Phylogenet Evol. 2015;91:68–85.
Mur LA, Allainguillaume J, Catalan P, Hasterok R, Jenkins G, et al. Exploiting the Brachypodium Tool Box in cereal and grass research. New Phytol. 2011;191:334–47.
Robertson IH. Chromosome numbers in Brachypodium Beauv. (Gramineae). Genetica. 1981;56:55–60.
Shi Y, Draper J, Stace CA. Ribosomal DNA variation and its phylogenetic implication in the genus Brachypodium (Poaceae). Plant Syst Evol. 1993;188:125–38.
Schippmann U. Brachypodium boissieri Nyman. An endemic grass species of southern Spain. Lagascalia. 1990;15:179–88.
Schippmann U. Revision der europäischen Arten der Gattung Brachypodium Palisot de Beauvois (Poaceae). Boissiera. 1991;45:1–250.
Scholz H. On the identity of Brachypodium firmifolium (Poaceae) from Cyprus. Willdenowia. 2007;37:215–20.
Schneider J, Winterfeld G, Hoffmann MH, Röser M. Duthieeae, a new tribe of grasses (Poaceae) identified among the early diverging lineages of subfamily Pooideae: molecular phylogenetics, morphological delineation, cytogenetics, and biogeography. Syst Biodiver. 2011;9:27–44.
Soltis DE, Soltis PS. Polyploidy: recurrent formation and genome evolution. Trends Ecol Evol. 1999;14:348–52.
Soltis DE, Buggs RJA, Doyle JJ, Soltis PS. What we still don’t know about polyploidy. Taxon. 2010;59:1387–403.
Steinwand MA, Young HA, Bragg JN, Tobias CM, Vogel JP. Brachypodium sylvaticum, a model for perennial grasses: transformation and inbred line development. PLoS One. 2013;8(9):e75180.
Vain P. Brachypodium as a model system for grass research. J Cereal Sci. 2011;54:1–7.
Valdés B, Scholz H.. Brachypodium genuense (DC.) Roem. & Schult. Euro+Med PlantNase—the information resource for Euro-Mediterranean plant diversity. 2009. http://ww2.bgbm.org/euroPlusMed/PTaxonDetail.asp?UUID=142AB795-174E-40A3-9787-9B1D435403FA.
Vogel JP, Tuna M, Budak H, Huo NX, Gu YQ, Steinwand MA. Development of SSR markers and analysis of diversity in Turkish populations of Brachypodium distachyon. BMC Plant Biol. 2009;9:88.
Warren DL, Glor RE, Turelli M. Environmental niche equivalency versus conservatism: quantitative approaches to niche evolution. Evolution. 2008;62:2868–83.
Watson L, Dallwitz MJ. The grass genera of the world. Wallingford, Oxon: CAB International; 1992.
Wolny E, Hasterok R. Comparative cytogenetic analysis of the genomes of the model grass Brachypodium distachyon and its close relatives. Ann Bot. 2009;104:873–81.
Wolny E, Lesniewska K, Hasterok R, Langdon T. Compact genomes and complex evolution in the genus Brachypodium. Chromosoma. 2011;120:199–212.
Zucol AF, Brea M, Bellosi E. Phytolith studies in Gran Barranca (central Patagonia, Argentina): middle and Late Eocene. In: Madden RH, Carlini AA, Vucetich MG, Kay RF, editors. The paleontology of Gran Barranca: evolution and environmental change through the Middle Cenozoic of Patagonia. Cambridge: Cambridge University Press; 2010. p. 317–40.
Author information
Authors and Affiliations
Corresponding author
Editor information
Editors and Affiliations
Rights and permissions
Copyright information
© 2015 Springer International Publishing Switzerland
About this chapter
Cite this chapter
Catalan, P., López-Álvarez, D., Díaz-Pérez, A., Sancho, R., López-Herránz, M.L. (2015). Phylogeny and Evolution of the Genus Brachypodium . In: Vogel, J. (eds) Genetics and Genomics of Brachypodium. Plant Genetics and Genomics: Crops and Models, vol 18. Springer, Cham. https://doi.org/10.1007/7397_2015_17
Download citation
DOI: https://doi.org/10.1007/7397_2015_17
Published:
Publisher Name: Springer, Cham
Print ISBN: 978-3-319-26942-9
Online ISBN: 978-3-319-26944-3
eBook Packages: Biomedical and Life SciencesBiomedical and Life Sciences (R0)