The Landscape of Micro-Inversions Provide Clues for Population Genetic Analysis of Humans
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ORIGINAL RESEARCH ARTICLE
The Landscape of Micro‑Inversions Provide Clues for Population Genetic Analysis of Humans Li Qu1,2 · Luotong Wang1,3 · Feifei He1,3 · Yilun Han1,3 · Longshu Yang1,3 · May D. Wang2 · Huaiqiu Zhu1,2,3 Received: 25 March 2020 / Revised: 2 September 2020 / Accepted: 3 September 2020 © The Author(s) 2020
Abstract Background Variations in the human genome have been studied extensively. However, little is known about the role of microinversions (MIs), generally defined as small ( 100 kb in length. Recently, small-scale inversions (with lengths much shorter than 10 kb) have been used in several studies for purposes, such as phylogenetic inference. These studies found an influence of small inversions on the formation of unusual flanking sequences in human and chimpanzee genomes [11] and developed tools to detect in-place inversions [12]. Nevertheless, the results of these studies were highly variable because of differences in the size used to define small inversions [13]. Moreover, current studies focus mainly on the differences in small inversions between human (Homo sapiens) and chimpanzee (Pan troglodytes) genomes [11], excluding the genomes of more distantly related primates, such as gorillas (Gorilla), orangutans (Pongo pygmaeus), gibbons (Hylobates sp.), baboons (Papio anubis), and rhesus macaques (Macaca mulatta). Among all the inversions of small size, the microinversions (MIs) [13], a type of extremely small inversions (generally East Asian. Notably, the African super-population had the most inverted alleles per individual at 3.96, while the East Asian population had the fewest at 3.03. The results displayed in both Fig. S3 and Fig. 3a are consistent with those of recent studies employing human SNP analysis [27, 35], in which the African super-population has the largest SNP number and the East Asian super-population has the smallest SNP number. In addition, a phylogenetic tree was constructed according to the MIs in gene regions for the five super-populations (see Fig. 3b). The result implies that the African super-population is distinct from the other 4 superpopulations. The descending order of the super-populations based on average inverted allele number and the clustering result also fit the Out of Africa hypothesis [29], which posits that humans originated in Africa and then modern Africans migrated to other continents. We will discuss this point further in the Discussion and conclusions section. Regarding the 26 populations, the average inverted allele count per individual populations ranged from 1.00 to 4.44 (see Table 1). Furthermore, the population of Americans of African Ancestry in the SW USA (ASW) had the most inverted alleles at 4.44, and the Chinese Dai in Xishuangbanna, China (CDX) had the least at 1.00. The geographic locations of the 26 populations are shown in Fig. 3c.
2.3 Population Structure Based on MI Statistics To examine the genetic structure of MIs hierarchically among populations, we constructed a genetic distancebased phylogenetic tree using all the MIs det
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