000079353 001__ 79353 000079353 005__ 20200117221658.0 000079353 0247_ $$2doi$$a10.1016/j.ympev.2018.06.003 000079353 0248_ $$2sideral$$a107042 000079353 037__ $$aART-2018-107042 000079353 041__ $$aeng 000079353 100__ $$aDíaz-Pérez, A.$$uUniversidad de Zaragoza 000079353 245__ $$aReconstructing the origins and the biogeography of species’ genomes in the highly reticulate allopolyploid-rich model grass genus Brachypodium using minimum evolution, coalescence and maximum likelihood approaches 000079353 260__ $$c2018 000079353 5060_ $$aAccess copy available to the general public$$fUnrestricted 000079353 5203_ $$aThe identification of homeologous genomes and the biogeographical analyses of highly reticulate allopolyploid-rich groups face the challenge of incorrectly inferring the genomic origins and the biogeographical patterns of the polyploids from unreliable strictly bifurcating trees. Here we reconstruct a plausible evolutionary scenario of the diverging and merging genomes inherited by the diploid and allopolyploid species and cytotypes of the model grass genus Brachypodium. We have identified the ancestral Brachypodium genomes and inferred the paleogeographical ranges for potential hybridization events that originated its allopolyploid taxa. We also constructed a comprehensive phylogeny of Brachypodium from five nuclear and plastid genes using Species Tree Minimum Evolution allele grafting and Species Network analysis. The divergence ages of the lineages were estimated from a consensus maximum clade credibility tree using fossil calibrations, whereas ages of origin of the diploid and allopolyploid species were inferred from coalescence Bayesian methods. The biogeographical events of the genomes were reconstructed using a stratified Dispersal-Extinction-Colonization model with three temporal windows. Our combined Minimum Evolution-coalescence-Bayesian approach allowed us to infer the origins and the identities of the homeologous genomes of the Brachypodium allopolyploids, matching the expected ploidy levels of the hybrids. To date, the current extant progenitor genomes (species) are only known for B. hybridum. Putative ancestral homeologous genome have been inherited by B. mexicanum, ancestral and recent genomes by B. boissieri, and only recently evolved genomes by B. retusum and the core perennial clade allopolyploids (B. phoenicoides, B. pinnatum 4x, B. rupestre 4x). We dissected the complex spatio-temporal evolution of ancestral and recent genomes and have detected successive splitting, dispersal and merging events for dysploid homeologous genomes in diverse geographical scenarios that have led to the current extant taxa. Our data support Mid-Miocene splits of the Holarctic ancestral genomes that preceded the Late Miocene origins of Brachypodium ancestors of the modern diploid species. Successive divergences of the annual B. stacei and B. distachyon diploid genomes were implied to have occurred in the Mediterranean region during the Late Miocene-Pliocene. By contrast, a profusion of splits, range expansions and different genome mergings were inferred for the perennial diploid genomes in the Mediterranean and Eurasian regions, with sporadic colonizations and further mergings in other continents during the Quaternary. A reliable biogeographical scenario was obtained for the Brachypodium genomes and allopolyploids where homeologous genomes split from their respective diploid counterpart lineages in the same ancestral areas, showing similar or distinct dispersals. By contrast, the allopolyploid taxa remained in the same ancestral ranges after hybridization and genome doubling events. Our approach should have utility in deciphering the genomic composition and the historical biogeography of other allopolyploid-rich organismal groups, which are predominant in eukaryotes. 000079353 536__ $$9info:eu-repo/grantAgreement/ES/DGA-FSE/Bioflora$$9info:eu-repo/grantAgreement/ES/MINECO/CGL2012-39953-C02-01$$9info:eu-repo/grantAgreement/ES/MINECO/CGL2016-79790-P 000079353 540__ $$9info:eu-repo/semantics/openAccess$$aby-nc-nd$$uhttp://creativecommons.org/licenses/by-nc-nd/3.0/es/ 000079353 590__ $$a3.992$$b2018 000079353 591__ $$aGENETICS & HEREDITY$$b42 / 174 = 0.241$$c2018$$dQ1$$eT1 000079353 591__ $$aEVOLUTIONARY BIOLOGY$$b12 / 50 = 0.24$$c2018$$dQ1$$eT1 000079353 591__ $$aBIOCHEMISTRY & MOLECULAR BIOLOGY$$b85 / 294 = 0.289$$c2018$$dQ2$$eT1 000079353 592__ $$a2.179$$b2018 000079353 593__ $$aEcology, Evolution, Behavior and Systematics$$c2018$$dQ1 000079353 593__ $$aMolecular Biology$$c2018$$dQ1 000079353 593__ $$aGenetics$$c2018$$dQ1 000079353 655_4 $$ainfo:eu-repo/semantics/article$$vinfo:eu-repo/semantics/acceptedVersion 000079353 700__ $$0(orcid)0000-0002-7734-8481$$aLópez-Álvarez, D. 000079353 700__ $$0(orcid)0000-0002-4845-4242$$aSancho, R. 000079353 700__ $$0(orcid)0000-0001-7793-5259$$aCatalán, P.$$uUniversidad de Zaragoza 000079353 7102_ $$15011$$2063$$aUniversidad de Zaragoza$$bDpto. CC.Agrar.y Medio Natural$$cÁrea Botánica 000079353 773__ $$g127 (2018), 256-271$$pMol. phylogenet. evol.$$tMOLECULAR PHYLOGENETICS AND EVOLUTION$$x1055-7903 000079353 8564_ $$s4428341$$uhttps://zaguan.unizar.es/record/79353/files/texto_completo.pdf$$yPostprint 000079353 8564_ $$s54257$$uhttps://zaguan.unizar.es/record/79353/files/texto_completo.jpg?subformat=icon$$xicon$$yPostprint 000079353 909CO $$ooai:zaguan.unizar.es:79353$$particulos$$pdriver 000079353 951__ $$a2020-01-17-22:12:05 000079353 980__ $$aARTICLE