Data from: Phenotypic resources immortalized in a panel of wild-derived strains of five species of house mice
Data files
Abstract
The house mouse, Mus musculus, is a widely used animal model in biomedical research, with classical laboratory strains (CLS) being the most frequently employed. However, the limited genetic variability in CLS hinders their applicability in evolutionary studies. Wild-derived strains (WDS), on the other hand, provide a suitable resource for such investigations. To assess the proportion of variation added by wild progenitors, we estimated phenotypic variation in 84 WDS representing 5 species (M. musculus, M. spretus, M. spicilegus, M. macedonicus, M. caroli), 3 subspecies (M. m. musculus, M. m. domesticus, M. m. castaneus), and compared it with 5 CLS. The spectrum of WDS captures long-term mouse evolution, estimated to be over 5 million years ago since the split of M. caroli from the remaining mouse species. All mice are housed in a conventional breeding facility (without a nanofilter barrier or specific-pathogen free condition) at the Institute of Vertebrate Biology, Czech Academy of Sciences, in Studenec. They are maintained under standard conditions: light/dark regime of 14/10 hours, temperatures of 23 ± 1 °C during summer (April-September) and 22 ± 1 °C during winter (October-March), respectively, and relative humidity within 40-70 %. Mice have access to food pellets and tap water ad libitum. Further data on this mouse repository and WDS can be obtained at https://housemice.cz/en/strains/.
Morphological traits were measured in 4335 mice and include body weight, spleen weight, body length, tail length, weight of both ovaries, sperm count, the weight of testes, left epididymis, and seminal vesicles. Reproductive ability was estimated in 87 WDS and 8 CLS. This dataset was obtained from 90,077 offspring born to 8,298 mothers in 17,049 litters recorded in Studenec studbooks between 2000 and 2023. Reproductive performance was characterized by litter size, newborn mortality (calculated as the proportion of stillborn or cannibalized mice across all litters), and the number of generations produced per year. We also estimated the time since a WDS was established from wild progenitors until completing 20 generations of strict brother-sister mating, i.e., the generation at which a strain of mice can be considered inbred.
Although CLS resemble M. m. domesticus and M. m. musculus WDS, they differ from them in 8 and 11 out of 15 phenotypic traits, respectively. The data suggest that WDS can be a useful tool in evolutionary studies, providing a basis for comparative analyses with other mammal taxa, particularly classical laboratory mice. The detected stunning phenotypic variation supplemented by genetic variation have great potential for medical applications.
README: Data from: Phenotypic resources immortalized in a panel of wild-derived strains of five species of house mice
[https://doi.org/10.5061/dryad.r7sqv9skn]
The dataset comprises five distinct datasets as detailed below:
Dataset 1: Dataset_1.Mitogenomes.Aligned.fasta
Contains aligned sequences of 163 whole mitochondrial genomes. The sequences were aligned using Clustal Omega SW (Sievers, Wilm et al. 2011: https://doi.org:10.1038/msb.2011.75 )
Dataset 2: Morphometric data of male mice
csv file contains raw morphometric data of 2363 male mice with columns:
“Genome” = Taxonomic status of the strain where mus = M. m. musculus, dom = M. m. domesticus, CLS = classical lab strain with predominantly M. m. domesticus genome, cas = M. m. castaneus, car = M. caroli, spi = M. spicilegus, spr = M. spretus, mac = M. macedonicus
“Strain” = wild-derived strain code
“PIN” = identification code of the mouse
“BW” = Body weight (g)
“L” = Body length (mm)
“LCd” = Tail length (mm)
“Tmass” = Mean testis weight (g)
“Epidydimis” = Weight of the left epidydimis (g)
“SemVes” = Weight of seminal vesicles (g)
“Sperm” = Number of sperm (millions)
“Tail.Body” = 100*Tail length/Body length
Dataset 2: Morphometric data of female mice
csv file contains raw morphometric data of 2131 female mice with columns:
“Genome” = Taxonomic status of the strain where mus = M. m. musculus, dom = M. m. domesticus, CLS = classical lab strain with predominantly M. m. domesticus genome, cas = M. m. castaneus, car = M. caroli, spi = M. spicilegus, spr = M. spretus, mac = M. macedonicus
“Strain” = wild-derived strain code
“PIN” = identification code of the mouse
“BW” = Body weight (g)
“L” = Body length (mm)
“LCd” = Tail length (mm)
“Ovary” = Ovary weight (g)
“Tail.Body” = 100*Tail length/Body length
Dataset 3: Spleen weight in mice
csv file contains raw data of 3229 mice with columns:
“Genome” = Taxonomic status of the strain where mus = M. m. musculus, dom = M. m. domesticus, CLS = classical lab strain with predominantly M. m. domesticus genome, cas = M. m. castaneus, car = M. caroli, spi = M. spicilegus, spr = M. spretus, mac = M. macedonicus
“Strain” = wild-derived strain code
“PIN” = identification code of the mouse
“Sex” = sex (coded as male or female)
“BW” = Body weight (g)
“Spleen” = Spleen length (g)
Dataset 4: Reproduction parameters
Contains summarized data on reproductive performance of 100 wild-derived and classical laboratory mouse strains with columns:
“Genome” = Taxonomic status of the strain where mus = M. m. musculus, dom = M. m. domesticus, CLS = classical lab strain with predominantly M. m. domesticus genome, cas = M. m. castaneus, car = M. caroli, spi = M. spicilegus, spr = M. spretus, mac = M. macedonicus
“Strain” = wild-derived strain code
“Start” = Date of birth or sampling
“N_Dams” = Number of females
“LitterSize” = Litter size
“SD” = Standard deviation (litter size)
“N_Litters” = Number of litters
“N_Mice” = Number of newborns
“Mortality” = Mortality in newborn mice
“DaysinLab” = Number of days spent in the lab (at the time of analysis - 1 June 2024)
“Gen” = Number of inbred generations weaned in Studenec
“Status” = Alive or extinct (on 1 June 2024)
“Gen_Year” = Mean number of generations per year
“Years2Inbred” = Estimated time in years to develop an inbred strain (at 20 generations of inbred mating)
Sharing/Access information
The dataset is associated with a publication titled "Phenogenomic resources immortalized in a panel of wild-derived strains of five species of house mice," authored by Piálek J., Ďureje Ľ., Hiadlovská Z., Kreisinger J., Aghová T., Bryjová A., Čížková D., Goüy de Bellocq J., Hejlová H., Janotová K., Martincová I., Orth A., Piálková J., Pospíšilová I., Rousková L., Vošlajerová Bímová B., Bonhomme F., Forejt J., Macholán M., Klusáčková P. The publication is available as a preprint on BioRxiv (https://doi.org/10.1101/2023.11.05.565684).
Methods
The first dataset contains 163 aligned mitogenome sequences. The measures presented in four csv files contaíning phenotype data were obtained from fresh mice immediately after sacrifice, and the units of variables are specified as millimeters (mm) for length measures and grams for mass measures.