Search

The origins of people in the Japanese archipelago are of long-standing interest among anthropologists, archeologists, linguists, and historians studying the history of Japan. While the ‘dual-structure’ model proposed by Hanihara in 1991 has been considered the primary working hypothesis for three decades, recent advances in DNA typing and sequencing technologies provide an unprecedented amount of present-day and ancient human nuclear genome data, which enable us to refine or extend the dual-structure model. In this review, we summarize recent genome sequencing efforts of present-day and ancient people in Asia, mostly focusing on East Asia, and we discuss the possible migration routes and admixture patterns of Japanese ancestors. We also report on a meta-analysis we performed by compiling publicly available datasets to clarify the genetic relationships of present-day and ancient Japanese populations with surrounding populations. Because the ancient genetic data from the Japanese archipelago have not yet been fully analyzed, we have to corroborate models of prehistoric human movement using not only new genetic data but also linguistic and archeological data to reconstruct a more comprehensive history of the Japanese people.

Background Transposable elements are biologically important components of eukaryote genomes. In particular, non-LTR retrotransposons (N-LTRrs) played a key role in shaping the human genome throughout evolution. In this study, we compared retrotransposon insertions differentially present in the genomes of Anatomically Modern Humans, Neanderthals, Denisovans and Chimpanzees, in order to assess the possible impact of retrotransposition in the differentiation of the human lineage. Results We first identified species-specific N-LTRrs and established their distribution in present day human populations. These analyses shortlisted a group of N-LTRr insertions that were found exclusively in Anatomically Modern Humans. These insertions are associated with an increase in the number of transcriptional/splicing variants of those genes they inserted in. The analysis of the functionality of genes containing human-specific N-LTRr insertions reflects changes that occurred during human evolution. In particular, the expression of genes containing the most recent N-LTRr insertions is enriched in the brain, especially in undifferentiated neurons, and these genes associate in networks related to neuron maturation and migration. Additionally, we identified candidate N-LTRr insertions that have likely produced new functional variants exclusive to modern humans, whose genomic loci show traces of positive selection. Conclusions Our results strongly suggest that N-LTRr impacted our differentiation as a species, most likely inducing an increase in neural complexity, and have been a constant source of genomic variability all throughout the evolution of the human lineage. Electronic supplementary material The online version of this article (10.1186/s13100-018-0133-4) contains supplementary material, which is available to authorized users.