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Germline Mutation Rates Differ Vastly Across Vertebrate Species; Show Sex Bias in Mammals, Birds

NEW YORK – An international team led by researchers in Denmark and China has found that germline mutation rates in vertebrates differ significantly between species, depending on generation time, age at maturity, fecundity, and other factors.

Germline mutation rates determine how quickly a species can evolve, but they have not been studied systematically across vertebrates except for a small number of species, according to the investigators.

For their study, published in Nature on Wednesday, the researchers sequenced the genomes of 151 parent-offspring trios from 68 species of mammals, fish, birds, and reptiles at 60X to 80X coverage using MGI Tech sequencing technology. The samples came from zoos, museums, research institutes, and farms across the world.

They then calculated the per-generation germline mutation rates by comparing the genomes of parents and offspring and found that they varied across species by a factor of 40.

Several life-history traits, such as maturation time, generation time, and number of offspring per generation, appeared to contribute to these differences, whereas other traits, such as longevity, mating strategy, and body mass, were not associated with germline mutation rates.

"While all the species have very different life-history traits, the germline mutation rate is quite conserved among species," said co-corresponding author Lucie Bergeron, an evolutionary biologist at the University of Copenhagen.

In addition, male mammals and birds tend to contribute more de novo germline mutations to their offspring than females, a sex bias that is apparently not present in reptiles and fish.

"We think it is due to the fact that there is more cell division in germ cells of males compared to females" [in mammals and birds], Bergeron said. "Females have eggs ready from birth while males produce sperm all their life. Therefore, mutations will accumulate in the male germline."

Reptiles and fish, on the other hand, produce sperm cells only during a limited time period before their mating season, reducing differences in cell division numbers between males and females, the authors wrote.

Among mammals, primates had the highest male bias whereas rodents had the lowest, indicating that generation time also had a role to play in germline mutation rates. 

"Species with longer generation intervals are expected to have higher per-generation mutation rates due to a combination of a larger number of cell divisions in spermatogenesis and more time for DNA damage to accumulate," the authors noted.

Another finding was that species with higher long-term effective population sizes tended to have lower mutation rates per generation, providing support for the so-called drift barrier hypothesis, which predicts that large populations have lower mutation rates because natural selection works more efficiently in them.

"This hypothesis was not tested earlier due to the lack of accurate mutation rate estimation. Our results provide insight into this hypothesis as we observed this negative correlation between effective population size and the per-generation [mutation] rates," Bergeron said.

In addition, her team found that domesticated species had much higher yearly germline mutation rates than wild ones, likely because they were bred to have shorter generation times and a lower reproductive age.

One limitation of the study was that some of the samples of non-domesticated species came from zoos, the authors wrote, which might have led to bias because zoo animals may have different generation times than wild animals.

While the researchers said that their study was among the first to directly calculate germline mutation rates by comparing parental and offspring genomes, they highlighted that more studies with bigger datasets are needed. "When we study more parent-offspring trios of the same species, we can find how mutation rates increase with parental age, which allows us to estimate more accurate germline mutation rates per generation," Bergeron said.