The long-standing interaction between viruses and hosts during evolution can have profound effects on the hosts. Recently, Chinese scientists have discovered an intriguing correlation between ancient viruses and the evolution of birds.
Researchers found that ancient viral sequences had once inserted into the DNA of birds, accompanying the species radiation of Passeriformes birds, and proliferating within avian hosts. Interestingly, birds not only efficiently eliminate proliferated viral DNA but sometimes also utilize residual viruses to modulate their own gene expression, such as those related to singing. This discovery was published in Nature Communications.
Embedded Viruses in the Genome
Among the over 10,000 extant bird species, more than 6,600 are Passeriformes birds, including familiar species like orioles, canaries, warblers, and sparrows.
Dr. Guangji Chen, the first author of the paper and a doctoral student at the University of Chinese Academy of Sciences, explained that Passeriformes birds, often referred to as "songbirds," are mostly proficient singers, with well-developed musculature for vocalization.
The origin of Passeriformes birds dates back approximately 50-70 million years ago, with a rapid radiation event around 22-40 million years ago, establishing the current diversity of species.
"We found evidence suggesting the involvement of ancient endogenous retrovirus (ERV) during the diversification of Passeriformes birds," said Chen to Chinese Science Bulletin.
So, what are endogenous retroviruses?
Dr. Shaohong Feng, the corresponding author of the paper and a researcher at the Life Evolution Research Center of Zhejiang University and the Liangzhu Laboratory, explained that certain retroviruses, after infecting host cells, have a probability of inserting their entire or partial DNA sequences into the host's genome, leaving traces of infection. If these sequences insert into the DNA of host germ cells, they may be inherited by offspring. Moreover, these viral sequences can be transcribed and expressed, functioning within host cells, which is referred to as endogenous retroviruses.
Contributing to Species Diversification and Innovative Capacities
Throughout evolution, a class of ERV-K sequence elements has been widely present in the genomes of Passeriformes birds, with a higher copy number in more recently emerged species.
"We found many ERV-K sequence elements in Passeriformes birds, inserted at different locations in their genomes, continuously influencing their genomic patterns during species divergence events. Even today, these endogenous viral sequences continue to proliferate within bird populations," said Feng.
Notably, during the Paleogene-Neogene boundary around 22-40 million years ago, ERV-K explosively appeared in Passeriformes birds, simultaneously invading the genomes of primates and other animal groups.
Although ERV-K sequence elements are "remnants" left by ancient viral infections, most no longer retain complete viral gene functions. However, some residual sequences have evolved to regulate gene expression switches in birds.
This study found that the expression of multiple genes in Passeriformes birds may be regulated by ERVK Solo-LTRs sequence elements.
"By comparing the brain gene expression of Passeriformes and non-Passeriformes birds, we were surprised to see that the ITGA2 gene exhibits high expression in the brain regions related to vocal learning in Passeriformes birds, while it shows lower expression in non-Passeriformes birds," said Chen. "A viral-derived sequence has inserted into the upstream region of this gene in Passeriformes, which may play a cis-regulatory role in its expression."
Based on this, the research team speculated that the continuous accumulation of ancient viruses not only provides innovative regulatory materials for songbirds but also promotes genetic and phenotypic diversity in Passeriformes birds during adaptive radiation.
"This not only enriches our understanding of the role of ancient viral sequences in avian evolution but also provides an example of how viral sequences regulate host gene functions, thus influencing host evolution," explained Feng.
The HVC, RA, and X are brain regions associated with the song control pathway in songbirds. High expression of the ITGA2 gene was detected in both the HVC and RA regions of the brain in the zebra finch. See the related paper for more information: link.
