A new paper published on 21 June in Science charts the genomes of 44 ruminants. Results of the large-scale study provide a valuable resource and plenty of insights into the evolution of mammalian biology. From deer and antelope to goats and cows, and even giraffes, ruminants thrive in various ecosystems around the world, and evolution has played a significant role.
Ruminants are a lineage of land-dwelling mammalian herbivores, including deer, cattle, buffalo, yaks, sheep, and goats, that live in diverse ecosystems around the world. The group of species first emerged some 32 to 39 million years ago and also form an important part of the global agricultural system.
However, origins and evolutionary relationships between species of the ruminant lineage remain contentious. The authors set out to better understand how evolution has shaped this incredibly diverse group of species using comparative phylogenomic approaches. In other words, comparing the evolutionary development and diversification of several species within this important group.
The team of researchers, led by Wen Wang and Guojie Zhang at the Kunming Institute of Zoology, and Rasmus Heller at the University of Copenhagen, Denmark, assembled the genomes of 44 species based on 40 trillion base pairs of raw DNA sequences. Then using the data to learn more about traits, such as heritable diseases, they generated a “family tree” by performing a so-called phylogenetic analysis.
Many of the 295 recently evolved genes are associated with the digestive system. Ruminants have specialized multi-compartment stomachs — comprised of the rumen, omasum and abomasum — to aid digestion. Most ruminants are herbivores and feed on plants full of difficult-to-digest cellulose. But multichambered stomachs enable them to ferment plants using stomach microbes and pass food back up for additional chewing.
In addition, a number of genes were linked to their so-called headgear — horns and antlers — which are typical of ruminants and used for mating and protection.
The newly sequenced genomes of ruminants may also provide insights into the human impact on these species. The researchers used methods to estimate that more than half of the ruminant species experienced dramatic population declines around the same time humans spread across the planet – around 100,000 to 50,000 years ago.
In addition, they were able to map species-level evolutionary changes. For example, giraffes, which are the tallest terrestrial animal, likely adapted to their Savannah environment. And out of 366 ruminant genes related to bone development, 115 of those have giraffe-specific mutations.
The study is part of the Earth BioGenome Project, a global effort to sequence the genetic code of all the planet’s eukaryotes – 1.5 million known species, including all plants, animals, protozoa, and fungi. The authors have also now established a public collection of the genomic and transcriptomic data called the Ruminant Genome Database.
Knowledge of genes and their variants could potentially help efforts towards the conservation of endangered species. And may also guide future farming practices aimed at mitigating the effects of climate change on agricultural commodities such as cattle. Moreover, animals could be bred to adapt better to warmer, drier climates.
(1) Chen, L. et al. Large-scale ruminant genome sequencing provides insights into their evolution and distinct traits. Science (2019). DOI: 10.1126/science.aav6202