Project description:Myanmar locates in the crossroads of South Asia, Southeast Asia, and East Asia, and is known for high culture diversity in different ethnic groups. It is considered to be important for understanding human evolutionary history and genetic diversity in East Eurasia. However, relatively few studies have examined the population structure and demographic history in Myanmar to date. In this study, we analyzed more than 220,000 genome-wide SNPs in 175 new samples of five ethnic groups from Myanmar and compared them with the published data. Our results showed that the Myanmar population is intricately substructured, with the main observed clusters corresponding roughly to western/northern highlanders (Chin, Naga, and Jingpo) and central/southern lowlanders (Bamar and Rakhine). The gene flow inferred from South Asia has a substantial influence (~11%) on the gene pool of central/southern lowlanders rather than western/northern highlanders. The genetic admixture is dated around 650 years ago. These findings suggest that the genome-wide variation in Myanmar was likely shaped by the linguistic, cultural, and historical changes.
Project description:Analyses of ancient DNA typically involve sequencing the surviving short oligonucleotides, and aligning to genome assemblies from related, modern species. Here, we report that skin from a female woolly mammoth (†Mammuthus primigenius) which died 52,000 years ago retained its ancient genome architecture. We use PaleoHi-C to map chromatin contacts and assemble its genome, yielding twenty-eight chromosome-length scaffolds. Chromosome territories, compartments, loops, Barr bodies, and inactive-X chromosome (Xi) superdomains persist. The active and inactive genome compartments in mammoth skin more closely resemble Asian elephant skin than other elephant tissues. Our analyses uncover new biology. Differences in compartmentalization reveal genes whose transcription was potentially altered in mammoths vs. elephants. Mammoth Xi has a tetradic architecture, not bipartite like human and mouse. We hypothesize that, shortly after this mammoth’s death, the sample spontaneously freeze-dried in the Siberian cold, leading to a glass transition that preserved subfossils of ancient chromosomes at nanometer scale.
Project description:The identity of most functional elements in the mammalian genome and the phenotypes they impact are unclear. Here, we perform a genome-wide comparative analysis of patterns of accelerated evolution in species with highly distinctive traits to discover candidate functional elements for clinically important phenotypes. We identify accelerated regions (ARs) in the elephant, hibernating bat, orca, dolphin, naked mole rat and thirteen-lined ground squirrel lineages in mammalian conserved regions, uncovering ~33,000 elements that bind hundreds of different regulatory proteins in humans and mice. ARs in the elephant, the largest land mammal, are uniquely enriched at elephant DNA damage response genes and changed conserved regulatory sites. The genomic hotspot for elephant ARs is the E3 ligase subunit of the Fanconi Anemia Complex, a master regulator of DNA repair. Additionally, ARs in the six species are associated with specific human clinical phenotypes that have apparent concordance with overt traits in each species.