Demographic modeling of admixed Latin American populations from whole genomes

A likelihood-based framework for demographic inference from genealogical trees

The demographic history of a population underlies patterns of genetic variation and is encoded in the gene-genealogical trees of the sampled haplotypes. Here we propose a demographic inference framework called the genealogical likelihood (gLike). Our method uses a graph-based structure to summarize the relationships among all lineages in a gene-genealogical tree with all possible trajectories of population memberships through time and derives the full likelihood across trees under a parameterized demographic model. We show through simulations and empirical applications that for populations that have experienced multiple admixtures, gLike can accurately estimate dozens of demographic parameters, including ancestral population sizes, admixture timing and admixture proportions, and it outperforms conventional demographic inference methods using the site frequency spectrum. Taken together, our proposed gLike framework harnesses underused genealogical information to offer high sensitivity and accuracy in inferring complex demographies for humans and other species.

Genetic diversity and dietary adaptations of the Central Plains Han Chinese population in East Asia

The Central Plains Han Chinese (CPHC) is the typical agricultural population of East Asia. Investigating the genome of the CPHC is crucial to understanding the genetic structure and adaptation of the modern humans in East Asia. Here, we perform whole genome sequencing of 492 CPHC individuals and obtained 22.65 million SNPs, 4.26 million INDELs and 41,959 SVs. We found the CPHC has a higher level of genetic diversity and the glycolipid metabolic genes show strong selection signals, e.g. LONP2, FADS2, FGF21 and SLC19A2. Ancient DNA analyses suggest that the domestication of crops, which drove the emergence of the candidate mutations. Notably, East Asian-specific SVs, e.g., DEL_21699 (LINC01749) and DEL_38406 (FAM102A) may be associated with the high prevalence of esophageal squamous carcinoma and primary angle-closure glaucoma. Our results provide an important genetic resource and show that dietary adaptations play an important role in phenotypic evolution in East Asian populations.

The Mexican Biobank Project promotes genetic discovery, inclusive science and local capacity building

Diversifying genotype-phenotype databases is essential to understanding complex trait and disease etiology across different environments and genetic ancestries. The rise of biobanks across the world is helping reveal the genetic and environmental architecture of multiple disease traits but the diversity they capture remains limited. To help close this gap, the Mexican Biobank (MXB) Project was recently generated, and has already revealed fine-scale genetic ancestries and demographic histories across the country, and their impact on trait-relevant genetic variation. This will help guide future genetic epidemiology and public health efforts, and has also improved polygenic prediction for several traits in Mexican populations compared with using data from other genome-wide association studies, such as the UK Biobank. The MXB illustrates the importance of transnational initiatives and funding calls that prioritize local leadership and capacity building to move towards inclusive genomic science.