Entirely unexpected differences in genome sizes and insertion-deletion patterns emerged after deep sequencing of three closely related American jay species.
Closely related species can show surprisingly large genetic differences. That is what American bioinformaticians and evolutionary biologists discovered by analysing no fewer than 45 individual genomes at high resolution from three jay species (Science, 12 December). The pangenomes of the widespread Woodhouse’s scrub jay (Aphelocoma woodhouseii), the Florida scrub jay (A. coerulescens), and the island scrub jay (A. insularis) – found only on Santa Cruz Island off California – obtained through long-read sequencing, show major differences in genome sizes, insertion-deletion patterns, and inversions. These include at least three million insertion-deletion polymorphisms and nearly 450,000 structural variants with more than three hundred inversions.
Differences in mutation types – such as insertions, deletions, translocations, or inversions – are associated with the demography of the birds. Inversions are most common in the most widespread species, whilst gene deletions occur most frequently in the species with the smallest population size. Transcriptome analyses show that this has detectable effects on the functioning of the jays. Outside humans and model species, relatively few DNA datasets are available that shed light on which mutations have occurred in wild populations – yet, according to the researchers, this is precisely what yields greater insight into the demographic effects on diversity and evolution.