Interest and controversy surrounding the evolutionary origins of extremely halophilic Archaea has increased in recent years, due to the discovery and characterization of the Nanohaloarchaea and the Methanonatronarchaeia. Initial attempts in explaining the evolutionary placement of the two new lineages in relation to the classical Halobacteria (also referred to as Haloarchaea) resulted in hypotheses that imply the new groups share a common ancestor with the Haloarchaea. However, more recent analyses have led to a shift: the Nanohaloarchaea have been largely accepted as being a member of the DPANN superphylum, outside of the euryarchaeota; whereas the Methanonatronarchaeia have been placed near the base of the Methanotecta (composed of the class II methanogens, the Halobacteriales, and Archaeoglobales). These opposing hypotheses have far-reaching implications on the concepts of convergent evolution (distantly related groups evolve similar strategies for survival), genome reduction, and gene transfer. In this work, we attempt to resolve these conflicts with phylogenetic and phylogenomic data. We provide a robust taxonomic sampling of Archaeal genomes that spans the Asgardarchaea, TACK Group, euryarchaeota, and the DPANN superphylum. In addition, we assembled draft genomes from seven new representatives of the Nanohaloarchaea from distinct geographic locations. Phylogenies derived from these data imply that the highly conserved ATP synthase catalytic/noncatalytic subunits of Nanohaloarchaea share a sisterhood relationship with the Haloarchaea. We also employ a novel gene family distance clustering strategy which shows this sisterhood relationship is not likely the result of a recent gene transfer. In addition, we present and evaluate data that argue for and against the monophyly of the DPANN superphylum, in particular, the inclusion of the Nanohaloarchaea in DPANN.

中文翻译：

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极端嗜盐古菌谱系的进化起源

近年来，由于纳米卤古生菌和甲烷二元古生菌的发现和表征，围绕极端嗜盐古生菌进化起源的兴趣和争议有所增加。解释这两个新谱系与经典盐杆菌（也称为盐古菌）的进化位置的最初尝试导致了暗示新群体与盐古菌有共同祖先的假设。然而，最近的分析导致了一个转变：纳米卤古菌在很大程度上被认为是 DPANN 超门的成员，在 euryarchaeota 之外。而 Methanonatronarchaeia 被放置在 Methanotecta 的底部附近（由 II 类产甲烷菌、Halobacteriales 和 Archaeoglobales 组成）。这些相反的假设对趋同进化（远相关的群体进化出相似的生存策略）、基因组减少和基因转移的概念具有深远的影响。在这项工作中，我们试图通过系统发育和系统发育数据来解决这些冲突。我们提供了涵盖 Asgardarchaea、TACK Group、euryarchaeota 和 DPANN 超门的古细菌基因组的强大分类样本。此外，我们组装了来自不同地理位置的纳米卤古菌的七个新代表的基因组草图。从这些数据得出的系统发育表明，纳米卤古菌的高度保守的 ATP 合酶催化/非催化亚基与卤古菌具有姐妹关系。我们还采用了一种新的基因家族距离聚类策略，表明这种姐妹关系不太可能是最近基因转移的结果。此外，我们提出和评估支持和反对 DPANN 超门单一系的数据，特别是在 DPANN 中包含 Nanohaloarchaea。