Bigger Doesn’t Mean Bolder: Testing the Pace-of-Life Syndrome Hypothesis of Four Wild Rodent Species to Novelty and Predation Risk

Background: Rodents, a globally distributed and diverse taxonomic group, have been the subjects of countless studies emulating risky situations. In controlled laboratory experiments the majority of focus has been on captive-bred rodents, whereas far less attention has been paid to their wild counterparts. Understanding how wild species respond to novel situations with associated risk can provide valuable information toward the pace-of-life syndrome hypothesis; if their behaviors are associated with a fast-slow continuum of life history. Additionally, whether wild populations of rodents embody adaptive capacity and behavioral repertoires, illustrated by habituation and variation in behavioral traits, respectively. Results: In this comparative study, we examined multiple behavioral responses of three native rodent species Mus caroli, Apodemus agrarius, Rattus losea, and one invasive, Rattus exulans, exposed to an unfamiliar microenvironment and novel cue from an allopatric predator, the leopard cat (Prionailurus bengalensis). All animals were captured and tested in a laboratory setting in Hualien County, Eastern Taiwan and subject to two consecutive nights of experimental trials. Behavioral responses to a novel situation during the first trial differed between species following the predictions of the pace-of-life syndrome; smaller species investing more time in non-defensive behaviors compared to the larger species. More specifically, the smaller species M. caroli and A. agrarius allocated more time to exploration and foraging, whereas the larger rat species R. exulans and R. losea spent more time motionless or concealing. During the second trial, leopard cat cues did not elicit antipredator behaviors, but rather, rodents were found to have opposing responses with increased non-defensive behaviors, specifically foraging efforts. Conclusions: Our results suggest that these four species do largely adhere to the pace-of-life syndrome with the two smaller mice species demonstrating increased boldness in a novel context compared to the larger rat species. Also, the wild populations of rodents in Eastern Taiwan may be naïve to leopard cats. Finally, the rodents in our study demonstrated habituation to the microenvironment, indicating they possess adaptive capacity.

Duplication and divergence of the retrovirus restriction gene Fv1 in Mus caroli mice allows protection from multiple retroviruses

Viruses and their hosts are locked in an evolutionary race where resistance to infection is acquired by the hosts while viruses develop strategies to circumvent these host defenses. Forming one arm of the host defense armory are cell autonomous restriction factors like Fv1. Originally described as protecting laboratory mice from infection by murine leukemia virus (MLV), Fv1s from some wild mice have also been found to restrict non-MLV retroviruses, suggesting an important role in the protection against viruses in nature. To begin to understand how restriction factors evolve, we surveyed the Fv1 genes of wild mice trapped in Thailand and characterized their restriction activities against a panel of retroviruses. An extra copy of the Fv1 gene, named Fv7, was found on chromosome 6 of three closely related Asian species of mice (Mus caroli, M. cervicolor and M. cookii). The presence of flanking repeats suggested it arose by LINE-mediated retrotransposition. A high degree of natural variation was observed in both Fv1 and Fv7, including numerous single nucleotide polymorphisms resulting in altered amino acids, as well as insertions and deletions that changed the length of the reading frames. These genes exhibited a range of restriction phenotypes with activities directed against feline foamy virus (FFV), equine infectious anemia virus (EIAV) and MLV. It seems likely, at least in the case of M. caroli, that the observed gene duplication confers protection against multiple viruses not possible with a single restriction factor. We suggest that EIAV-, FFV- and MLV-like viruses are endemic within these populations, driving the evolution of the Fv1 and Fv7 genes.Author SummaryDuring the passage of time all vertebrates will be exposed to infection by a variety of different kinds of virus. To meet this threat, a variety of genes for natural resistance to viral infection have evolved. The prototype of such so-called restriction factors is encoded by the mouse Fv1 gene, which acts to block the life cycle of retroviruses at a stage between virus entry into the cell and integration of the viral genetic material into the nuclear DNA. We have studied the evolution of this gene in certain species of wild mice from South East Asia and describe an example where a duplication of the Fv1 gene has taken place. The two copies of the gene, initially identical, have evolved separately allowing the development of resistance to two rather different kinds of retroviruses, lentiviruses and spumaviruses. Independent selection for resistance to these two kinds of retrovirus suggests that such mice are repeatedly exposed to never-before-reported pathogenic retroviruses of these genera.

Repeat associated mechanisms of genome evolution and function revealed by the Mus caroli and Mus pahari genomes

ABSTRACTUnderstanding the mechanisms driving lineage-specific evolution in both primates and rodents has been hindered by the lack of sister clades with a similar phylogenetic structure having high-quality genome assemblies. Here, we have created chromosome-level assemblies of the Mus caroli and Mus pahari genomes. Together with the Mus musculus and Rattus norvegicus genomes, this set of rodent genomes is similar in divergence times to the Hominidae (human-chimpanzee-gorilla-orangutan). By comparing the evolutionary dynamics between the Muridae and Hominidae, we identified punctate events of chromosome reshuffling that shaped the ancestral karyotype of Mus musculus and Mus caroli between 3 to 6 MYA, but that are absent in the Hominidae. In fact, Hominidae show between four-and seven-fold lower rates of nucleotide change and feature turnover in both neutral and functional sequences suggesting an underlying coherence to the Muridae acceleration. Our system of matched, high-quality genome assemblies revealed how specific classes of repeats can play lineage-specific roles in related species. For example, recent LINE activity has remodeled protein-coding loci to a greater extent across the Muridae than the Hominidae, with functional consequences at the species level such as reproductive isolation. Furthermore, we charted a Muridae-specific retrotransposon expansion at unprecedented resolution, revealing how a single nucleotide mutation transformed a specific SINE element into an active CTCF binding site carrier specifically in Mus caroli. This process resulted in thousands of novel, species-specific CTCF binding sites. Our results demonstrate that the comparison of matched phylogenetic sets of genomes will be an increasingly powerful strategy for understanding mammalian biology.

Chromosome assembly of large and complex genomes using multiple references

Despite the rapid development of sequencing technologies, assembly of mammalian-scale genomes into complete chromosomes remains one of the most challenging problems in bioinformatics. To help address this difficulty, we developed Ragout, a reference-assisted assembly tool that now works for large and complex genomes. Taking one or more target assemblies (generated from an NGS assembler) and one or multiple related reference genomes, Ragout infers the evolutionary relationships between the genomes and builds the final assemblies using a genome rearrangement approach. Using Ragout, we transformed NGS assemblies of 15 different Mus musculus and one Mus spretus genomes into sets of complete chromosomes, leaving less than 5% of sequence unlocalized per set. Various benchmarks, including PCR testing and realigning of long PacBio reads, suggest only a small number of structural errors in the final assemblies, comparable with direct assembly approaches. Additionally, we applied Ragout to Mus caroli and Mus pahari genomes, which exhibit karyotype-scale variations compared to other genomes from the Muridae family. Chromosome color maps confirmed most large-scale rearrangements that Ragout detected.