Genomic resources for wild populations of the house mouse, Mus musculus and its close relative Mus spretus

WOS: 000390231600001PubMed ID: 27622383Wild populations of the house mouse (Mus musculus) represent the raw genetic material for the classical inbred strains in biomedical research and are a major model system for evolutionary biology. We provide whole genome sequencing data of individuals representing natural populations of M. m. domesticus (24 individuals from 3 populations), M. m. helgolandicus (3 individuals), M. m. musculus (22 individuals from 3 populations) and M. spretus (8 individuals from one population). We use a single pipeline to map and call variants for these individuals and also include 10 additional individuals of M. m. castaneus for which genomic data are publically available. In addition, RNAseq data were obtained from 10 tissues of up to eight adult individuals from each of the three M. m. domesticus populations for which genomic data were collected. Data and analyses are presented via tracks viewable in the UCSC or IGV genome browsers. We also provide information on available outbred stocks and instructions on how to keep them in the laboratory.Max-Planck Society; DFG [HA 3139/4-1]; ERC [322564]; contract-research-project for the Bundeswehr Medical Service [M/SABX/005]This work was mostly financed by institutional resources of the Max-Planck Society, a DFG grant to B.H. and M.T. (HA 3139/4-1) and an ERC grant to D.T. (NewGenes, 322564). We thank Sonja Ihle, Susanne Krochter, Ruth Rottscheidt for contributing to collecting animals in the wild and our animal care takers for active involvement of optimizing the scheme for wild mouse keeping. The initial analysis of mice from Afghanistan was funded by contract-research-project for the Bundeswehr Medical Service M/SABX/005. We thank Bastian Pfeifer for help with software package PopGenome, Leslie Turner for discussion and Daniel M. Hooper and Trevor Price for helpful comments on the manuscript. D.T. had full access to all the data in the study and take responsibility for the integrity of the data and the accuracy of the data analysis

Cross-Species Single-Cell Analysis Reveals Divergence of the Primate Microglia Program

Summary Microglia, the brain-resident immune cells, are critically involved in many physiological and pathological brain processes, including neurodegeneration. Here we characterize microglia morphology and transcriptional programs across ten species spanning more than 450 million years of evolution. We find that microglia express a conserved core gene program of orthologous genes from rodents to humans, including ligands and receptors associated with interactions between glia and neurons. In most species, microglia show a single dominant transcriptional state, whereas human microglia display significant heterogeneity. In addition, we observed notable differences in several gene modules of rodents compared with primate microglia, including complement, phagocytic, and susceptibility genes to neurodegeneration, such as Alzheimer’s and Parkinson’s disease. Our study provides an essential resource of conserved and divergent microglia pathways across evolution, with important implications for future development of microglia-based therapies in humans

Communication at the Garden Fence – Context Dependent Vocalization in Female House Mice

<div><p>House mice (<i>Mus musculus</i>) live in social groups where they frequently interact with conspecifics, thus communication (<i>e</i>.<i>g</i>. chemical and/or auditory) is essential. It is commonly known that male and female mice produce complex vocalizations in the ultrasonic range (USV) that remind of high-pitched birdsong (so called mouse song) which is mainly used in social interactions. Earlier studies suggest that mice use their USVs for mate attraction and mate choice, but they could also be used as signal during hierarchy establishment and familiarization, or other communication purposes. In this study we elucidated the vocalization behaviour of interacting female mice over an extended period of time under semi-natural conditions. We asked, if the rate or structure of female vocalization differs between different social and non-social contexts. We found that female USV is mainly used in social contexts, driven by direct communication to an unknown individual, the rate of which is decreased over time by a familiarization process. In addition we could show that female mice use two distinct types of USVs, differing in their frequency, which they use differently depending on whether they directly or indirectly communicate with another female. This supports the notion that vocalization in mice is context dependent, driven by a reasonable and yet underestimated amount of complexity that also involves the interplay between different sensory signals, like chemical and auditory cues.</p></div

Syllables in different context regions.

<p>a) The first two linear discriminant functions (LD) of syllable parameters in different context regions in nights without direct contact (night 1). b) The first two linear discriminant functions (LD) of syllable parameters in different context regions in nights with direct contact (nights 2, 3, 4). Ellipses in the scatterplots show the 95% confidence interval around the group means. The contribution of the two linear discriminants is given below the axis. Arrows indicate the direction of the most influencing parameters on the separation of the data; for the loadings of these and the other syllable parameters see <a href="http://www.plosone.org/article/info:doi/10.1371/journal.pone.0152255#pone.0152255.t003" target="_blank">Table 3b and 3c</a>.</p

Principal component analysis of syllable types.

<p>Scatter plots are based on the spectral parameters of the main analysis (see <a href="http://www.plosone.org/article/info:doi/10.1371/journal.pone.0097244#pone-0097244-t001" target="_blank">table 1</a>). <b>a</b> Jump syllable types. 1^st principal component (PC) distinguishes between early and late jumps, 2^nd PC distinguishes between upward and downward jumps. <b>b</b> All non-jump syllable types. 1^st PC distinguishes between upward and downward frequency modulations, 2^nd PC distinguishes between u-shaped and inverse-u-shape frequency modulations. For explanation of abbreviations see <a href="http://www.plosone.org/article/info:doi/10.1371/journal.pone.0097244#pone-0097244-t002" target="_blank">table 2</a>.</p

Comparison of the repeat number distribution of syllable types.

<p>Presented are graphs for the syllable types (a) JED (Jump-early-down, for details see <a href="http://www.plosone.org/article/info:doi/10.1371/journal.pone.0097244#pone-0097244-t002" target="_blank">Table 2</a>) and (b) SDN (Simple-down), with separate graphs for each group (FRA = French, GER = German, f = female, m = male). The solid black lines show the distribution of repeat numbers in the observed syllable sequences (orig). The dotted green and dashed yellow lines show the distribution of repeat numbers in the syllable sequences calculated with the Probability model (PM) and with the Markov model (MM) respectively.</p

Frequency-distribution of the Center of Gravity of syllable frequency.

<p>Data for night 1 (without direct contact) are shown in the upper panel, data for nights 2–4 (with direct contact) in the lower panel. The vertical line is drawn at 45 kHz and separates low-frequency and high-frequency syllables.</p

Discriminant function analysis of syllable parameters in the different social contexts.

<p>Scatter plots are separated by sex and population. Arrows indicate the direction of the three parameters with the strongest influence on the separation of the data: slope, jumps, turns; plus and minus indicate a positive or negative change of the parameter in the arrow's direction; for the loadings of these and the other parameters see <a href="http://www.plosone.org/article/info:doi/10.1371/journal.pone.0097244#pone-0097244-t005" target="_blank">table 5</a>. Abbreviations and colours as in <a href="http://www.plosone.org/article/info:doi/10.1371/journal.pone.0097244#pone-0097244-g004" target="_blank">Figure 4</a>.</p

Songs and syllables in the different recording nights.

<p>a) The number of songs per night for each individual pair of females from sets A and B, as well as the mean number of songs per night in sets A and B. b) The mean number of songs in the different context regions in the four recording nights. c) The first two linear discriminant functions (LD) of syllable parameters in different recording nights. Ellipses show the 95% confidence interval around the group means. The contribution of the two linear discriminants is given below the axis. Arrows indicate the direction of the most influencing parameters on the separation of the data; for the loadings of these and the other syllable parameters see <a href="http://www.plosone.org/article/info:doi/10.1371/journal.pone.0152255#pone.0152255.t003" target="_blank">Table 3a</a>.</p

The experimental set-up.

<p>a) Photo of the arena set-up with one animal at the contact window (red circle). b) The contact window when closed and c) the open contact window. d) Schematic view of the arena with context regions as used for video scoring. The standard equipment for the experiments is colored in grey, the context regions that were used for video scoring are marked in different colors and inscribed with following abbreviations: CC = contact corners (dark blue); CR = contact region (light blue); CW = contact window (turquoise); F = food; FR = food region (green); H = red Plexiglas house; M = microphone, hanging from the top (see a); MB = male bedding (red); NR = neutral region (yellow); W = water.</p