Genome-scale phylogenetic analysis finds extensive gene transfer among fungi

Although the role of lateral gene transfer is well recognized in the evolution of bacteria, it is generally assumed that it has had less influence among eukaryotes. To explore this hypothesis, we compare the dynamics of genome evolution in two groups of organisms: cyanobacteria and fungi. Ancestral genomes are inferred in both clades using two types of methods: first, Count, a gene tree unaware method that models gene duplications, gains and losses to explain the observed numbers of genes present in a genome; second, ALE, a more recent gene tree-aware method that reconciles gene trees with a species tree using a model of gene duplication, loss and transfer. We compare their merits and their ability to quantify the role of transfers, and assess the impact of taxonomic sampling on their inferences. We present what we believe is compelling evidence that gene transfer plays a significant role in the evolution of fungi.

尽管水平基因转移（Lateral Gene Transfer）在细菌演化中的作用已得到广泛认可，但学界普遍认为其对真核生物演化的影响相对有限。为验证这一假说，我们对蓝细菌与真菌两类生物的基因组演化动态开展对比分析。我们采用两种方法对两个进化枝的祖先基因组进行推断：其一为Count工具，这是一种不依赖基因树的方法，通过构建基因重复、获得与丢失的模型来解释基因组中观测到的基因数量；其二为ALE工具，这是一种更前沿的依赖基因树的方法，通过整合基因重复、丢失与转移的模型，实现基因树与物种树的协调适配。我们对比了这两种方法的优劣及其量化基因转移作用的能力，并评估了分类学采样对其推断结果的影响。本研究提供了确凿无疑的证据，证明基因转移在真菌演化中发挥了重要作用。