Data from: Large-scale ruminant genome sequencing provides insights into their evolution and distinct traits

The ruminants are one of the most successful mammalian lineages,
exhibiting morphological and habitat diversity and containing several key
livestock species. To better understand their evolution, we generated and
analyzed de novo assembled genomes of 44 ruminant species, representing
all six Ruminantia families. We used these genomes to create a
time-calibrated phylogeny to resolve topological controversies, overcoming
the challenges of incomplete lineage sorting. Population dynamic analyses
show that population declines commenced between 100,000 and 50,000 years
ago, which is concomitant with expansion in human populations. We also
reveal genes and regulatory elements that possibly contribute to the
evolution of the digestive system, cranial appendages, immune system,
metabolism, body size, cursorial locomotion, and dentition of the
ruminants.