Insights into human genetic variation and population history from 929 diverse genomes.

Genome sequences from diverse human groups are needed to understand the structure of genetic variation in our species and the history of, and relationships between, different populations. We present 929 high-coverage genome sequences from 54 diverse human populations, 26 of which are physically phased using linked-read sequencing. Analyses of these genomes reveal an excess of previously undocumented common genetic variation private to southern Africa, central Africa, Oceania, and the Americas, but an absence of such variants fixed between major geographical regions. We also find deep and gradual population separations within Africa, contrasting population size histories between hunter-gatherer and agriculturalist groups in the past 10,000 years, and a contrast between single Neanderthal but multiple Denisovan source populations contributing to present-day human populations.Wellcome grants 098051 and 206194, and S.A.M. and R.D. also by Wellcome grant 207492. A.B. and P.S. were supported by the Francis Crick Institute (FC001595) which receives its core funding from Cancer Research UK, the UK Medical Research Council and the Wellcome Trust. P.S. was also supported by the European Research Council (grant no. 852558) and the Wellcome Trust (217223/Z/19/Z). R.H. was supported by a Gates Cambridge scholarship. P.H. was supported by Estonian Research Council Grant PUT1036. D.R. is an Investigator of the Howard Hughes Medical Institute

How Fish Population Genomics Can Promote Sustainable Fisheries: A Road Map

Maintenance of genetic diversity in marine fishes targeted by commercial fishing is a grand challenge for the future. Most of these species are abundant and therefore important for marine ecosystems and food security. Here, we present a road map of how population genomics can promote sustainable fisheries. In these species, the development of reference genomes and whole genome sequencing is key, because genetic differentiation at neutral loci is usually low due to large population sizes and gene flow. First, baseline allele frequencies representing genetically differentiated populations within species must be established. These can then be used to accurately determine the composition of mixed samples, forming the basis for population demographic analysis to inform sustainably set fish quotas. SNP-chip analysis is a cost-effective method for determining baseline allele frequencies and for population identification in mixed samples. Finally, we describe how genetic marker analysis can transform stock identification and management

Asian horses deepen the MSY phylogeny.

Humans have shaped the population history of the horse ever since domestication about 5500 years ago. Comparative analyses of the Y chromosome can illuminate the paternal origin of modern horse breeds. This may also reveal different breeding strategies that led to the formation of extant breeds. Recently, a horse Y-chromosomal phylogeny of modern horses based on 1.46 Mb of the male-specific Y (MSY) was generated. We extended this dataset with 52 samples from five European, two American and seven Asian breeds. As in the previous study, almost all modern European horses fall into a crown group, connected via a few autochthonous Northern European lineages to the outgroup, the Przewalski's Horse. In total, we now distinguish 42 MSY haplotypes determined by 158 variants within domestic horses. Asian horses show much higher diversity than previously found in European breeds. The Asian breeds also introduce a deep split to the phylogeny, preliminarily dated to 5527 ± 872 years. We conclude that the deep splitting Asian Y haplotypes are remnants of a far more diverse ancient horse population, whose haplotypes were lost in other lineages

Volumetric cell-and-portal generation

We present an algorithm to generate a cell-and-portal decomposition of general indoor scenes. The method is an adaptation of the 3D watershed transform, computed on a distance-to-geometry sampled field. The watershed is processed using a flooding analogy in the distance field space. Flooding originates from local minima, each minimum producing a region. Portals are built as needed to avoid the merging of regions during their growth. As a result, the cell-and-portal decomposition is closely linked to the structure of the models. In a building, the algorithm finds all the rooms, doors and windows. To restrict the memory load, a hierarchical implementation of the algorithm is presented. We also explain how to handle possible model degeneracies -such as cracks, holes and interpenetrating geometries- using a pre-voxelisation step. The hierarchical algorithm, preceded when necessary by the pre-voxelisation, was tested on a large range of models. We show that it is able to deal with classical architectural models, as well as cave-like environments and large mixed indoor/outdoor scenes. Thanks to the intermediate distance field representation, the algorithm can be used regardless of the way the model is represented: it deals with parametric curves, implicit surfaces, volumetric data and polygon soups in a unified way.SCOPUS: cp.jFLWINinfo:eu-repo/semantics/publishe