How and why overcome the impediments to resolution: lessons from rhinolophid and hipposiderid bats.
How and why overcome the impediments to resolution: lessons from rhinolophid and hipposiderid bats.
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DOI：
10.1093/molbev/msu329
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发表时间：
2015-02
影响因子：
10.7
通讯作者：
Teeling EC
中科院分区：
文献类型：
--
作者：
Foley NM;Thong VD;Soisook P;Goodman SM;Armstrong KN;Jacobs DS;Puechmaille SJ;Teeling EC
旧大陆叶鼻蝙蝠与相近的马蹄铁蝙蝠之间的系统发育和分类关系尚不清楚。在这项研究中，我们生成了一个新的大约10-kb的分子数据集，包含了40个蝙蝠物种的19个核外显子和内含子基因片段，以阐明犀牛科和河马科之间的系统发育关系。我们估计了分化时间，并探讨了任何不一致的系统发育信号的潜在原因。我们展示了异常分类群和基因对系统发育重建的影响，并比较了内含子和外显子数据的相对性能，以解决系统发育关系。系统发育分析产生了一个很好的系统发育，支持了海马科的家族地位，并证明了最大的属，海马属的类。经过化石校准的时间表和生物地理分析估计，犀牛科和河马科在始新世大约42 Ma的非洲分化。系统谱、时间表和一个独特的反转录转座子插入支持将亚部落Rhinonycterina提升到家族水平，并在此诊断。多样化率的比较分析表明，中中新世气候最适期，犀牛属和河马属经历了物种多样化。内含子与外显子的对比分析表明，内含子为我们的最优树提供了更好的节点支持，这对于大规模系统基因组学研究来说是一个重要的发现，这些研究通常只依赖于外显子数据。随着最近由一种新型冠状病毒引起的中东呼吸综合征的爆发，对这些物种的研究迫在眉睫，因为它们被认为是紧急严重急性呼吸综合征（SARS）样冠状病毒的天然宿主。研究表明，宿主系统发育是决定病毒持久性和复制能力的主要因素，并可作为新出现疾病的预测因子。因此，这一新解决的系统发育可用于指导未来对病毒多样性的评估，并阐明哺乳动物中sars样冠状病毒的起源和发展。
The phylogenetic and taxonomic relationships among the Old World leaf-nosed bats (Hipposideridae) and the closely related horseshoe bats (Rhinolophidae) remain unresolved. In this study, we generated a novel approximately 10-kb molecular data set of 19 nuclear exon and intron gene fragments for 40 bat species to elucidate the phylogenetic relationships within the families Rhinolophidae and Hipposideridae. We estimated divergence times and explored potential reasons for any incongruent phylogenetic signal. We demonstrated the effects of outlier taxa and genes on phylogenetic reconstructions and compared the relative performance of intron and exon data to resolve phylogenetic relationships. Phylogenetic analyses produced a well-resolved phylogeny, supporting the familial status of Hipposideridae and demonstrated the paraphyly of the largest genus, Hipposideros. A fossil-calibrated timetree and biogeographical analyses estimated that Rhinolophidae and Hipposideridae diverged in Africa during the Eocene approximately 42 Ma. The phylogram, the timetree, and a unique retrotransposon insertion supported the elevation of the subtribe Rhinonycterina to family level and which is diagnosed herein. Comparative analysis of diversification rates showed that the speciose genera Rhinolophus and Hipposideros underwent diversification during the Mid-Miocene Climatic Optimum. The intron versus exon analyses demonstrated the improved nodal support provided by introns for our optimal tree, an important finding for large-scale phylogenomic studies, which typically rely on exon data alone. With the recent outbreak of Middle East respiratory syndrome, caused by a novel coronavirus, the study of these species is urgent as they are considered the natural reservoir for emergent severe acute respiratory syndrome (SARS)-like coronaviruses. It has been shown that host phylogeny is the primary factor that determines a virus’s persistence, replicative ability, and can act as a predictor of new emerging disease. Therefore, this newly resolved phylogeny can be used to direct future assessments of viral diversity and to elucidate the origin and development of SARS-like coronaviruses in mammals.