Additional Information of our paper
Authors: Isaac Babarinde and Naruya Saitou
Title: The dynamics, causes, and impacts of mammalian evolutionary rates revealed bythe analyses of capybara draft genome sequences
Published in Genome Biology and Evolution on August 24, 2020
Website: https://academic.oup.com/gbe/advance-article/doi/10.1093/gbe/evaa157/5896529
DOI: https://doi.org/10.1093/gbe/evaa157
AbstractCapybara (Hydrochoerus hydrochaeri) is an extant rodent species with the highest body weight. The
draft genome of capybara was sequenced and the estimated genome size was 2.6 Gbp. Although thebody size of capybara is about 60 times that of guinea pig, comparative analyses revealed that theneutral evolutionary rates of the two species were not substantially different. However, analyses of 39
genomes revealed very heterogeneous evolutionary rates. The highest evolutionary rate, 8.5 times higher
than the human rate, was found in the Cricetidae-Muridae common ancestor after the divergence ofSpalacidae. Muridae, the family with the highest number of species among mammals, emerged after therate acceleration. Factors responsible for the evolutionary rate heterogeneity was investigated throughcorrelations between the evolutionary rate and longevity, gestation length, litter frequency, litter size,
body weight, generation interval, age at maturity, and taxonomic order. The regression analysis of thesefactors showed that the model with three factors (taxonomic order, generation interval and litter size)
had the highest predictive power (R2 = 0. 74). These three factors determine the number of meiosis perunit time. We also conducted transcriptome analysis, and found that the evolutionary rate dynamics
affects the evolution of gene expression patterns.

Note: Abstract in Journal website has one error in line 3: 2.7 should be 2.6 (shown inred).

Dr. Isaac Babarinde

Professor Naruya Saitou

1Capybara individual (male) “Rai” when he was alive; died inMarch 2015. This photo was provided by Izu Shaboten Park.
In spring of 2015, Dr. Wen-Hsiung Li, Director of Academia
Sinica Biodiversity Research Center at that time, visited NIG
Saitou Laboratory. We discussed about evolutionary rate
heterogeneity among mammals. Because body size wasconsidered to be negatively correlated with the evolutionary rateof the species, we got interested in capybara that has the largest
body size among the extant rodents. Saitou rememberedcapybaras in hot spring in Izu Shaboten Park in Sizuoka
prefecture, and phoned that park immediately. Fortunately, one
individual named Rai passed away one week ago, and they promised Saitou to dig that body up.
Saitou and Dr. Babarinde, who was at that time Ph.D. student in Saitou Laboratory, visited Izu
Shaboten Park and received small muscle piece of Rai. Dr. Babarinde extracted Rai’s DNA in SaitouLab, and that was used for draft genome sequencing conducted in Professor Ituro Inoue’s HumanGenetics Laboratory at National Institute of Genetics, using Next Generation Sequencer MiSeq. It took
us more than four years to complete data analysis, and finally our paper was published in Genome
Biology and Evolution. Coincidentally, Dr. Wen-Hsiung Li handled our paper as associate editor of thisjournal. This is the first report of de novo genome sequencing from our laboratory. Please look at ourpaper about our findings.
Future perspectives
We are interested in genomic regions responsible for morphological characters among diverse mammals.
For example, capybara’s tail is vestigial as in hominoids. We hope to find these parallelism inmorphology from genome sequence comparison.

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