Identifying population histories, adaptive genes, and genetic duplication from population-scale next generation sequencing

摘要: The arrival of next-generation sequencing (NGS) technologies in the mid 2000s opened the floodgates to a massive amount of genetic data. Not only does NGS permit relatively easy access to the genome of nearly any species, it also enables sequencing highly degraded DNA characteristic of ancient samples and museum specimens. The representation of genomic data across the tree of life has been spreading rapidly over the past decade owing to the emergence of numerous methods for inexpensively sequencing entire genomes and reduced representations of genomes based on NGS. However, without any high-quality preexisting genomic resources, species with large, highly paralogous genomes pose a major obstacle for NGS because accurately assembling short read data becomes extremely challenging. Furthermore, reads derived from paralogs will likely map to the same locus, which can inflate …