Institut National de la Recherche Agronomique, Centre de Montpellier, UMR Diversité et Adaptation des Plantes Cultivées, Domaine de Melgueil, 34130 Mauguio, France.
BMC Evol Biol. 2011 Jun 24;11:181. doi: 10.1186/1471-2148-11-181.
Introgressive 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. Grasses of the Triticeae tribe provide a particularly striking example of incongruence among gene trees. Previous phylogenies, mostly inferred with one gene, are in conflict for several taxon positions. Therefore, obtaining a resolved picture of relationships among genera and species of this tribe has been a challenging task. Here, we obtain the most comprehensive molecular dataset to date in Triticeae, including one chloroplastic and 26 nuclear genes. We 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.
We obtain resolved phylogenetic hypotheses using the supermatrix and Bayesian Concordance Factors (BCF) approaches despite numerous incongruences among gene trees. These phylogenies suggest the existence of 4-5 major clades within Triticeae, with Psathyrostachys and Hordeum being the deepest genera. In addition, we construct a multigenic network that highlights parts of the Triticeae history that have not evolved in a tree-like manner. Dasypyrum, Heteranthelium and genera of clade V, grouping Secale, Taeniatherum, Triticum and Aegilops, have evolved in a reticulated manner. Their relationships are thus better represented by the multigenic network than by the supermatrix or BCF trees. Noteworthy, we demonstrate that gene-tree incongruences increase with genetic distance and are greater in telomeric than centromeric genes. Together, our results suggest that recombination is the main factor decoupling gene trees from multigenic trees.
Our study is the first to propose a comprehensive, multigenic phylogeny of Triticeae. It clarifies several aspects of the relationships among genera and species of this tribe, and pinpoints biological groups with likely reticulate evolution. Importantly, this study extends previous results obtained in Drosophila by demonstrating that recombination can exacerbate gene-tree conflicts in phylogenetic reconstructions.
渐渗事件（例如杂交、基因流、水平基因转移）和祖先多态性的不完全谱系分选对系统发育分析来说是一个挑战，因为不同的基因可能表现出相互矛盾的系统发育历史。小麦族的禾本科植物提供了一个特别引人注目的例子，说明基因树之间存在不一致。以前的系统发育，主要是根据一个基因推断的，对于几个分类群的位置存在冲突。因此，获得这个族属和种之间关系的清晰图像一直是一项具有挑战性的任务。在这里，我们获得了迄今为止在小麦族中最全面的分子数据集，包括一个叶绿体和 26 个核基因。我们旨在检验在面对（潜在的）大规模渐渗事件和/或不完全谱系分选的情况下是否有可能推断出系统发育关系；确定没有以树状方式进化的进化历史部分；并解释这个族属中基因树冲突的生物学原因。
尽管基因树之间存在许多不一致，但我们使用超级矩阵和贝叶斯一致性因子（BCF）方法获得了分辨率较高的系统发育假设。这些系统发育表明，小麦族内存在 4-5 个主要分支，其中冰草和大麦是最深的属。此外，我们构建了一个多基因网络，突出了小麦族历史中没有以树状方式进化的部分。粗山羊草、异皮蝇属和 V 分支的属，包括黑麦、垂穗披碱草、小麦和山羊草，以网状方式进化。因此，它们的关系通过多基因网络比超级矩阵或 BCF 树更好地表示。值得注意的是，我们证明基因树的不一致性随着遗传距离的增加而增加，并且在端粒基因中比着丝粒基因更大。总之，我们的结果表明，重组是使基因树与多基因树分离的主要因素。
我们的研究首次提出了一个全面的、多基因的小麦族系统发育。它澄清了这个族属和种之间关系的几个方面，并指出了可能具有网状进化的生物群体。重要的是，这项研究通过证明重组可以在系统发育重建中加剧基因树冲突，扩展了以前在果蝇中获得的结果。
