@article{fdi:010053717,
  title = {{M}ultigenic phylogeny and analysis of tree incongruences in {T}riticeae ({P}oaceae)},
  author = {{E}scobar, {J}. {S}. and {S}cornavacca, {C}. and {C}enci, {A}lberto and {G}uilhaumon, {C}. and {S}antoni, {S}. and {D}ouzery, {E}. {J}. {P}. and {R}anwez, {V}. and {G}lemin, {S}. and {D}avid, {J}.},
  editor = {},
  language = {{ENG}},
  abstract = {{B}ackground: {I}ntrogressive events (e.g., hybridization, gene flow, horizontal gene transfer) and incomplete lineage sorting of ancestral polymorphisms are a challenge for phylogenetic analyses since different genes may exhibit conflicting genealogical histories. {G}rasses of the {T}riticeae tribe provide a particularly striking example of incongruence among gene trees. {P}revious phylogenies, mostly inferred with one gene, are in conflict for several taxon positions. {T}herefore, obtaining a resolved picture of relationships among genera and species of this tribe has been a challenging task. {H}ere, we obtain the most comprehensive molecular dataset to date in {T}riticeae, including one chloroplastic and 26 nuclear genes. {W}e aim to test whether it is possible to infer phylogenetic relationships in the face of (potentially) large-scale introgressive events and/or incomplete lineage sorting; to identify parts of the evolutionary history that have not evolved in a tree-like manner; and to decipher the biological causes of gene-tree conflicts in this tribe. {R}esults: {W}e obtain resolved phylogenetic hypotheses using the supermatrix and {B}ayesian {C}oncordance {F}actors ({BCF}) approaches despite numerous incongruences among gene trees. {T}hese phylogenies suggest the existence of 4-5 major clades within {T}riticeae, with {P}sathyrostachys and {H}ordeum being the deepest genera. {I}n addition, we construct a multigenic network that highlights parts of the {T}riticeae history that have not evolved in a tree-like manner. {D}asypyrum, {H}eteranthelium and genera of clade {V}, grouping {S}ecale, {T}aeniatherum, {T}riticum and {A}egilops, have evolved in a reticulated manner. {T}heir relationships are thus better represented by the multigenic network than by the supermatrix or {BCF} trees. {N}oteworthy, we demonstrate that gene-tree incongruences increase with genetic distance and are greater in telomeric than centromeric genes. {T}ogether, our results suggest that recombination is the main factor decoupling gene trees from multigenic trees. {C}onclusions: {O}ur study is the first to propose a comprehensive, multigenic phylogeny of {T}riticeae. {I}t clarifies several aspects of the relationships among genera and species of this tribe, and pinpoints biological groups with likely reticulate evolution. {I}mportantly, this study extends previous results obtained in {D}rosophila by demonstrating that recombination can exacerbate gene-tree conflicts in phylogenetic reconstructions.},
  keywords = {},
  booktitle = {},
  journal = {{B}mc {E}volutionary {B}iology},
  volume = {11},
  numero = {},
  pages = {181},
  ISSN = {1471-2148},
  year = {2011},
  DOI = {10.1186/1471-2148-11-181},
  URL = {https://www.documentation.ird.fr/hor/fdi:010053717},
}