genome-wide data

全基因组数据
  • 文章类型: Case Reports
    许多动物的传统分类,包括鸟类,高度依赖于外部形态特征,如羽毛颜色。然而,生物声学和遗传或基因组数据都彻底改变了我们对某些谱系关系的理解,并导致了全面的分类重组。在这项研究中,我们介绍了一个在物种丰富的捕蝇亚科Niltavinae中错误地划定属边界的案例。历史上,该亚科中的属是根据蓝色和棕色男性身体羽毛划定的,直到最近基于一些线粒体和核基因座的研究发现了几例通用分类错误。在这里,我们使用来自43个物种的广泛生物声学数据和来自28个物种的基因组数据对Niltavinae中的物种进行了基本重新分类。我们的研究表明,即使在属级别上,歌曲也是对这些鸟类进行分类的重要特征,而羽毛性状表现出充分的收敛性,并导致了许多历史性的错误归因。我们的分类学重组导致了主要属的新生物地理限制,这样,Cyornis属现在只能向东延伸到苏拉威西岛,秀拉,还有Banggai,而Eumyias被重新定义为远远超出华莱士线延伸到塞拉姆和帝汶岛。我们的结论建议不要过度依赖形态特征,并强调了整合数据集的重要性。
    Traditional classification of many animals, including birds, has been highly dependent on external morphological characters like plumage coloration. However, both bioacoustics and genetic or genomic data have revolutionized our understanding of the relationships of certain lineages and led to sweeping taxonomic re-organizations. In this study, we present a case of erroneous delimitation of genus boundaries in the species-rich flycatcher subfamily Niltavinae. Genera within this subfamily have historically been delineated based on blue versus brown male body plumage until recent studies based on a few mitochondrial and nuclear loci unearthed several cases of generic misclassification. Here we use extensive bioacoustic data from 43 species and genomic data from 28 species for a fundamental reclassification of species in the Niltavinae. Our study reveals that song is an important trait to classify these birds even at the genus level, whereas plumage traits exhibit ample convergence and have led to numerous historic misattributions. Our taxonomic re-organization leads to new biogeographic limits of major genera, such that the genus Cyornis now only extends as far east as the islands of Sulawesi, Sula, and Banggai, whereas Eumyias is redefined to extend far beyond Wallace\'s Line to the islands of Seram and Timor. Our conclusions advise against an over-reliance on morphological traits and underscore the importance of integrative datasets.
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  • 文章类型: Journal Article
    蒙古族人口超过600万,是中国讲蒙古语的人口最多的国家。然而,由于样本数量有限且单核苷酸多态性(SNP)覆盖率较低,因此蒙古人的遗传结构和混合史仍不清楚。在这项研究中,我们对来自辽宁省阜新市的38个蒙古族个体的700,000多个SNP的全基因组数据进行基因分型,以基于典型和先进的群体遗传分析方法[主成分分析(PCA),掺合料,FST,f3-统计,f4-统计,qpAdm/qpWave,qpGraph,ALDER,和TreeMix]。我们发现阜新蒙古族与汉族有着密切的遗传关系,北部蒙古人,其他讲蒙古语的人,和东亚地区的通古西人。此外,我们发现黄河流域和西辽河流域的新石器时代的小米农民和蒙古高原和阿穆尔河流域的新石器时代的狩猎采集者是主要的祖先来源,在阜新蒙古人的基因库中,还有其他与欧亚草原牧民和新石器时代伊朗农民有关的基因流。这些结果揭示了动态的人口历史,复杂的人口混合物,阜新蒙古族遗传多样性的多种来源。
    The Mongolian population exceeds six million and is the largest population among the Mongolic speakers in China. However, the genetic structure and admixture history of the Mongolians are still unclear due to the limited number of samples and lower coverage of single-nucleotide polymorphism (SNP). In this study, we genotyped genome-wide data of over 700,000 SNPs in 38 Mongolian individuals from Fuxin in Liaoning Province to explore the genetic structure and population history based on typical and advanced population genetic analysis methods [principal component analysis (PCA), admixture, FST, f 3 -statistics, f 4 -statistics, qpAdm/qpWave, qpGraph, ALDER, and TreeMix]. We found that Fuxin Mongolians had a close genetic relationship with Han people, northern Mongolians, other Mongolic speakers, and Tungusic speakers in East Asia. Also, we found that Neolithic millet farmers in the Yellow River Basin and West Liao River Basin and Neolithic hunter-gatherers in the Mongolian Plateau and Amur River Basin were the dominant ancestral sources, and there were additional gene flows related to Eurasian Steppe pastoralists and Neolithic Iranian farmers in the gene pool of Fuxin Mongolians. These results shed light on dynamic demographic history, complex population admixture, and multiple sources of genetic diversity in Fuxin Mongolians.
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  • 文章类型: Journal Article
    Trans-Eurasian cultural and genetic exchanges have significantly influenced the demographic dynamics of Eurasian populations. The Hexi Corridor, located along the southeastern edge of the Eurasian steppe, served as an important passage of the ancient Silk Road in Northwest China and intensified the transcontinental exchange and interaction between populations on the Central Plain and in Western Eurasia. Historical and archeological records indicate that the Western Eurasian cultural elements were largely brought into North China via this geographical corridor, but there is debate on the extent to which the spread of barley/wheat agriculture into North China and subsequent Bronze Age cultural and technological mixture/shifts were achieved by the movement of people or dissemination of ideas. Here, we presented higher-resolution genome-wide autosomal and uniparental Y/mtDNA SNP or STR data for 599 northwestern Han Chinese individuals and conducted 2 different comprehensive genetic studies among Neolithic-to-present-day Eurasians. Genetic studies based on lower-resolution STR markers via PCA, STRUCTURE, and phylogenetic trees showed that northwestern Han Chinese individuals had increased genetic homogeneity relative to northern Mongolic/Turkic/Tungusic speakers and Tibeto-Burman groups. The genomic signature constructed based on modern/ancient DNA further illustrated that the primary ancestry of the northwestern Han was derived from northern millet farmer ancestors, which was consistent with the hypothesis of Han origin in North China and more recent northwestward population expansion. This was subsequently confirmed via excess shared derived alleles in f3/f4 statistical analyses and by more northern East Asian-related ancestry in the qpAdm/qpGraph models. Interestingly, we identified one western Eurasian admixture signature that was present in northwestern Han but absent from southern Han, with an admixture time dated to approximately 1000 CE (Tang and Song dynasties). Generally, we provided supporting evidence that historic Trans-Eurasian communication was primarily maintained through population movement, not simply cultural diffusion. The observed population dynamics in northwestern Han Chinese not only support the North China origin hypothesis but also reflect the multiple sources of the genetic diversity observed in this population.
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