Accuracy of allele frequency estimation using pooled RNA-Seq.

For nonmodel organisms, genome-wide information that describes functionally relevant variation may be obtained by RNA-Seq following de novo transcriptome assembly. While sequencing has become relatively inexpensive, the preparation of a large number of sequencing libraries remains prohibitively expensive for population genetic analyses of nonmodel species. Pooling samples may be then an attractive alternative. To test whether pooled RNA-Seq accurately predicts true allele frequencies, we analysed the liver transcriptomes of 10 bank voles. Each sample was sequenced both as an individually barcoded library and as a part of a pool. Equal amounts of total RNA from each vole were pooled prior to mRNA selection and library construction. Reads were mapped onto the de novo assembled reference transcriptome. High-quality genotypes for individual voles, determined for 23,682 SNPs, provided information on 'true' allele frequencies; allele frequencies estimated from the pool were then compared with these values. 'True' frequencies and those estimated from the pool were highly correlated. Mean relative estimation error was 21% and did not depend on expression level. However, we also observed a minor effect of interindividual variation in gene expression and allele-specific gene expression influencing allele frequency estimation accuracy. Moreover, we observed strong negative relationship between minor allele frequency and relative estimation error. Our results indicate that pooled RNA-Seq exhibits accuracy comparable with pooled genome resequencing, but variation in expression level between individuals should be assessed and accounted for. This should help in taking account the difference in accuracy between conservatively expressed transcripts and these which are variable in expression level.

Maternal-care behavior and life-history traits in house mice (Mus domesticus) artificially selected for high voluntary wheel-running activity.

To test the hypothesis that selective breeding for high voluntary wheel running negatively affects maternal performance in house mice, we observed maternal behavior and compared litter size and mass, in replicate lines of selected (N=4) and control (N=4) mice from generations 20 and 21 of an artificial selection experiment. At generation 21, selected-line females ran 2.8-times more revolutions per day than females from random-bred control lines, when tested at approximately 6 weeks of age as part of the normal selection protocol. After giving birth, dams from selected and control lines exhibited similar frequencies of maternal behaviors and also spent similar amounts of time in general locomotor activity at litter ages of both 9 and 16 days. Dams from selected lines also performed equally well as controls in repeated pup-retrieval trials. At first parturition, selected-line dams averaged 2.4 g smaller in body mass as compared with dams from the control lines; however, neither litter size nor litter mass at birth (generation 20) or at weaning (generation 21) differed significantly between selected and control lines. We conclude that, at least under the husbandry conditions employed, maternal behavior and reproductive output at first parturition are genetically independent of wheel-running behavior.

Maximum cold-induced food consumption in mice selected for high locomotor activity: implications for the evolution of endotherm energy budgets.

We studied house mice (Mus domesticus) that had been artificially selected for high activity to test the hypothesis that a high capacity for energy assimilation in cold-exposed endotherms could evolve as a correlated response to selection for increased locomotor activity. After 10 generations of selection for increased voluntary wheel-running, mice from four selected lines ran 75 % more wheel revolutions per day than did mice from four random-bred, control lines. The maximum cold-induced rates of food consumption (C(max); mean 10.6 g day(-1)) and energy assimilation (A(max); mean 141 kJ day(-1)) were not significantly higher in the selected than in the control mice. However, in cold-exposure trials, mice from the selected lines maintained body mass better than did mice from the control lines. C(max) and A(max) were positively correlated with the amount of wheel-running activity measured before cold-exposure and also with the rates of food consumption measured when the mice had access to running wheels. In females at least, the correlation was significant not only among individuals but also among adjusted means of the replicate lines, which suggests the presence of a positive genetic correlation between the traits. Thus, despite the lack of a significant difference between the selected and control lines in maximum rate of food consumption, the remaining results conform to the hypothesis that a selection for increased locomotor activity could be a factor behind the evolution of the ability to sustain activity and maintain energy balance during prolonged cold-exposure, as occurred during the evolution of mammalian and avian endothermy.

Food consumption and body composition in mice selected for high wheel-running activity.

The effects of genetic selection for high wheel running (13th generation) and prolonged access (8 weeks) to running wheels on food consumption and body composition were studied in house mice (Mus domesticus). Mice from four replicate lines selected for high wheel-running activity ran over twice as many revolutions per day on activity wheels as did mice from four replicate control lines. At approximately 49 days of age, all mice were placed individually in cages with access to wheels and monitored for 6 days, after which wheels were prevented from rotating for the "sedentary" individuals. During the experiment, five feeding trials were conducted and body mass was measured weekly. After 8 weeks, body composition was measured by hydrogen isotope dilution. Across the five feeding trials, mice in the "active" group (wheels free to rotate) consumed 22.4% more food than mice in the "sedentary" group (wheels locked); mice from the selected lines consumed 8.4% more food than mice from the control lines (average of all trials; body mass-corrected values). In females, but not males, we found a significant interaction between selection and wheel access treatments: within the "active" group the difference in food consumption between selected and control animals was greater than in the "sedentary" group. At the end of the study, mice from the "active" and "sedentary" groups did not differ significantly in body mass; however, mice from the selected lines were approximately 6% smaller in body mass. Estimated lean body mass did not differ significantly either between selected and control lines or between wheel-access groups (P>0.3). Mice from selected lines had lower total body fat compared to mice from control lines (P=0.05; 24.5% reduction; LSMEANS) as did mice from the "active" compared to "sedentary" group (P= 0.03; 29.2% reduction; LSMEANS). Under these conditions, a sufficient explanation for the difference in body mass between the selected and control lines was the difference in fat content.

Body temperatures of house mice artificially selected for high voluntary wheel-running behavior: repeatability and effect of genetic selection.

We studied rectal body temperatures of house mice (Mus domesticus) that had been artificially selected for high voluntary wheel running.1. At generation 17, mice from the four replicate selected lines ran, on average, 2.5-times as many revolutions/day as did mice from the four random-bred control lines.2. During the day, repeatability of individual differences in body temperature measured 4 days apart was low; at night, repeatability was statistically significant across three time scales (1 day, 1 week, 2 weeks).3. During the day, body temperatures of selected and control animals did not differ; at night, mice from selected lines had higher body temperatures. However, when amount of wheel running immediately prior to measurement was included as a covariate, the difference was no longer statistically significant.Higher body temperatures, associated with increased activity, might enhance locomotor abilities through Q10 effects, increase metabolic rate and food requirements, affect sleep patterns, and alter expression of heat-shock proteins.

Energy assimilation, parental care and the evolution of endothermy.

The question of the selection forces which initiated the evolution of endothermy in birds and mammals is one of the most intriguing in the evolutionary physiology of vertebrates. Many students regard the aerobic capacity model as the most plausible hypothesis. This paper presents an alternative model, in which the evolution of endothermy in birds and mammals was driven by two factors: (i) a selection for intense post-hatching parental care, particularly feeding offspring, and (ii) the high cost of maintaining the increased capacity of the visceral organs necessary to support high rates of total daily energy expenditures.

Behaviour of house mice artificially selected for high levels of voluntary wheel running.

We have developed a novel model to study the correlated evolution of behavioural and morphophysiological traits in response to selection for increased locomotor activity. We used selective breeding to increase levels of voluntary wheel running in four replicate lines of laboratory house mice, Mus domesticus, with four random-bred lines maintained as controls. The experiment presented here tested for correlated behavioural responses in the wheel-cage complex, with wheels either free to rotate or locked (environmental factor). After 13 generations, mice from selected lines ran 2.2 times as many revolutions/day as controls on days 5 and 6 of initial exposure to wheels (10 826 versus 4890 revolutions/day, corresponding to 12.1 and 5.5 km/day, respectively). This increase was caused primarily by mice from selected lines running faster, not more minutes per day. Focal-animal observations confirmed that the increase in revolutions/day involved more actual running (or climbing in locked wheels), not an increase in coasting (or hanging). Not surprisingly, access to free versus locked wheels had several effects on behaviour, including total time spent in wheels, sniffing and biting. However, few behaviours showed statistically significant differences between the selected and control lines. Selection did not increase the total time spent in wheels (either free or locked), the frequency of nonlocomotor activities performed in the wheels, nor the amount of locomotor activity in cages attached to the wheels; as well, selection did not decrease the amount of time spent sleeping. Thus, wheel running is, at the genetic level, a largely independent axis of behaviour. Moreover, the genetic architecture of overall wheel running and its components seem conducive to increasing total distance moved without unduly increasing energy or time-related costs. The selection experiment also offers a new approach to study the proximate mechanisms of wheel-running behaviour itself. For example, frequencies of sniffing and wire biting were reduced in selected females but not males. This result suggests that motivation or function of wheel running may differ between the sexes. Copyright 1999 The Association for the Study of Animal Behaviour.

Artificial selection for increased wheel-running activity in house mice results in decreased body mass at maturity.

To test the hypothesis that body size and activity levels are negatively genetically correlated, we conducted an artificial selection experiment for increased voluntary wheel-running activity in house mice (Mus domesticus). Here, we compare body masses of mice from control and selected lines after 14 generations of selection. In both groups, beginning at weaning and then for 8 weeks, we housed half of the individuals with access to running wheels that were free to rotate and the other half with wheels that were locked to prevent rotation. Mice from selected lines were more active than controls at weaning (21 days) and across the experiment (total revolutions during last week: females 2.5-fold higher, males 2.1-fold higher). At weaning, mice from selected and control lines did not differ significantly in body mass. At 79 days of age, mice from selected lines weighed 13.6 % less than mice from control lines, whereas mice with access to free wheels weighed 4.5 % less than 'sedentary' individuals; both effects were statistically significant and additive. Within the free-wheel-access group, individual variation in body mass of males was negatively correlated with amount of wheel-running during the last week (P<0.01); for females, the relationship was also negative but not statistically significant (P>0.40). The narrow-sense genetic correlation between wheel-running and body mass after 8 weeks of wheel access was estimated to be -0. 50. A negative genetic correlation could account for the negative relationship between voluntary wheel-running and body mass that has been reported across 13 species of muroid rodents.

Energy cost of wheel running in house mice: implications for coadaptation of locomotion and energy budgets.

Laboratory house mice (Mus domesticus) that had experienced 10 generations of artificial selection for high levels of voluntary wheel running ran about 70% more total revolutions per day than did mice from random-bred control lines. The difference resulted primarily from increased average velocities rather than from increased time spent running. Within all eight lines (four selected, four control), females ran more than males. Average daily running distances ranged from 4.4 km in control males to 11.6 km in selected females. Whole-animal food consumption was statistically indistinguishable in the selected and control lines. However, mice from selected lines averaged approximately 10% smaller in body mass, and mass-adjusted food consumption was 4% higher in selected lines than in controls. The incremental cost of locomotion (grams food/revolution), computed as the partial regression slope of food consumption on revolutions run per day, did not differ between selected and control mice. On a 24-h basis, the total incremental cost of running (covering a distance) amounted to only 4.4% of food consumption in the control lines and 7.5% in the selected ones. However, the daily incremental cost of time active is higher (15.4% and 13.1% of total food consumption in selected and control lines, respectively). If wheel running in the selected lines continues to increase mainly by increases in velocity, then constraints related to energy acquisition are unlikely to be an important factor limiting further selective gain. More generally, our results suggest that, in small mammals, a substantial evolutionary increase in daily movement distances can be achieved by increasing running speed, without remarkable increases in total energy expenditure.

On the relation between basal and maximum metabolic rate in mammals.

Basal and maximum metabolic rates, measured by oxygen consumption, for 18 species of wild mammals have been obtained from a search of literature records. The mass exponent of the allometric regression equation for maximum metabolic rate is significantly higher than that for BMR (0.841 and 0.745, respectively; P less than 0.05) in the group of animals examined. No significant correlation between mass-independent basal and maximum metabolic rates has been found. These results do not support the 'aerobic capacity' model of the origin of endothermy.