A Selective Sweep on a Deleterious Mutation in CPT1A in Arctic Populations

Arctic populations live in an environment characterized by extreme cold and the absence of plant foods for much of the year and are likely to have undergone genetic adaptations to these environmental conditions in the time they have been living there. Genome-wide selection scans based on genotype data from native Siberians have previously highlighted a 3 Mb chromosome 11 region containing 79 protein-coding genes as the strongest candidates for positive selection in Northeast Siberians. However, it was not possible to determine which of the genes might be driving the selection signal. Here, using whole-genome high-coverage sequence data, we identified the most likely causative variant as a nonsynonymous G>A transition (rs80356779; c.1436C>T [p.Pro479Leu] on the reverse strand) in CPT1A, a key regulator of mitochondrial long-chain fatty-acid oxidation. Remarkably, the derived allele is associated with hypoketotic hypoglycemia and high infant mortality yet occurs at high frequency in Canadian and Greenland Inuits and was also found at 68% frequency in our Northeast Siberian sample. We provide evidence of one of the strongest selective sweeps reported in humans; this sweep has driven this variant to high frequency in circum-Arctic populations within the last 6–23 ka despite associated deleterious consequences, possibly as a result of the selective advantage it originally provided to either a high-fat diet or a cold environment.     

Size‐related life‐history traits in geometrid moths: a comparison of a temperate and a tropical community

1. Comparative studies on insect life histories are facilitated by the increasing availability of reliable phylogenies but are hampered by the scarcity of comparable data. Fortunately, morphological proxies of some life‐history traits can be measured on preserved specimens. 2. This study compared values of size‐related life‐history traits among a tropical (Ugandan) and a temperate (Estonian) assemblage of geometrid moths. 3. A comparative analysis based on an originally derived phylogeny revealed that tropical moths were, on average, larger than temperate ones. Tropical moths also had somewhat lower relative abdomen masses than temperate ones. This indicates that the tropical rather than the temperate moths tend to use an income (rather than capital) breeding strategy. Nevertheless, no difference was found in a related index of pro‐ovigeny. When body size was accounted for, tropical moths were found to lay smaller eggs than temperate ones. 4. The differences between the two compared areas are consistent with selection on higher mobility of the moths imposed by the more diverse tropical vegetation. Relatively larger eggs of temperate moths may constitute an adaptation to overcome the presumably stronger quantitative defences of their host plants. 5. Overall, however, we conclude that the differences in ecologically relevant size‐related traits are relatively low among moth assemblages of a tropical and a temperate forest region, indicating that these environments may not impose radically different selective pressures on insect life histories.     

The influence of natural barriers in shaping the genetic structure of Maharashtra populations

Background

The geographical position of Maharashtra state makes it rather essential to study the dispersal of modern humans in South Asia. Several hypotheses have been proposed to explain the cultural, linguistic and geographical affinity of the populations living in Maharashtra state with other South Asian populations. The genetic origin of populations living in this state is poorly understood and hitherto been described at low molecular resolution level.

Methodology/Principal Findings

To address this issue, we have analyzed the mitochondrial DNA (mtDNA) of 185 individuals and NRY (non-recombining region of Y chromosome) of 98 individuals belonging to two major tribal populations of Maharashtra, and compared their molecular variations with that of 54 South Asian contemporary populations of adjacent states. Inter and intra population comparisons reveal that the maternal gene pool of Maharashtra state populations is composed of mainly South Asian haplogroups with traces of east and west Eurasian haplogroups, while the paternal haplogroups comprise the South Asian as well as signature of near eastern specific haplogroup J2a.

Conclusions/Significance

Our analysis suggests that Indian populations, including Maharashtra state, are largely derived from Paleolithic ancient settlers; however, a more recent (∼10 Ky older) detectable paternal gene flow from west Asia is well reflected in the present study. These findings reveal movement of populations to Maharashtra through the western coast rather than mainland where Western Ghats-Vindhya Mountains and Narmada-Tapti rivers might have acted as a natural barrier. Comparing the Maharastrian populations with other South Asian populations reveals that they have a closer affinity with the South Indian than with the Central Indian populations.     

Counterintuitive size patterns in bivoltine moths: late-season larvae grow larger despite lower food quality

Within a season, successive generations of short-lived organisms experience different combinations of environmental parameters, such as temperature, food quality and mortality risk. Adult body size of e.g. insects is therefore expected to vary both as a consequence of proximate environmental effects as well as adaptive responses to seasonal cues. In this study, we examined intraspecific differences in body size between successive generations in 12 temperate bivoltine moths (Lepidoptera), with the ultimate goal to critically compare the role of proximate and adaptive mechanisms in determining seasonal size differences. In nearly all species, individuals developing late in the season (diapausing generation) attained a larger adult size than their conspecifics with the larval period early in the season (directly developing generation) despite the typically lower food quality in late summer. Rearing experiments conducted on one of the studied species, Selenia tetralunaria also largely exclude the possibility that the proximate effects of food quality and temperature are decisive in determining size differences between successive generations. Adaptive explanations appear likely instead: the larger body size in the diapausing generation may be adaptively associated with the lower bird predation pressure late in the season, and/or the likely advantage of large pupal size during overwintering.     

The western and eastern roots of the Saami--the story of genetic "outliers" told by mitochondrial DNA and Y chromosomes

The Saami are regarded as extreme genetic outliers among European populations. In this study, a high-resolution phylogenetic analysis of Saami genetic heritage was undertaken in a comprehensive context, through use of maternally inherited mitochondrial DNA (mtDNA) and paternally inherited Y-chromosomal variation. DNA variants present in the Saami were compared with those found in Europe and Siberia, through use of both new and previously published data from 445 Saami and 17,096 western Eurasian and Siberian mtDNA samples, as well as 127 Saami and 2,840 western Eurasian and Siberian Y-chromosome samples. It was shown that the “Saami motif” variant of mtDNA haplogroup U5b is present in a large area outside Scandinavia. A detailed phylogeographic analysis of one of the predominant Saami mtDNA haplogroups, U5b1b, which also includes the lineages of the “Saami motif,” was undertaken in 31 populations. The results indicate that the origin of U5b1b, as for the other predominant Saami haplogroup, V, is most likely in western, rather than eastern, Europe. Furthermore, an additional haplogroup (H1) spread among the Saami was virtually absent in 781 Samoyed and Ob-Ugric Siberians but was present in western and central European populations. The Y-chromosomal variety in the Saami is also consistent with their European ancestry. It suggests that the large genetic separation of the Saami from other Europeans is best explained by assuming that the Saami are descendants of a narrow, distinctive subset of Europeans. In particular, no evidence of a significant directional gene flow from extant aboriginal Siberian populations into the haploid gene pools of the Saami was found.     

Distinguishing between anticipatory and responsive plasticity in a seasonally polyphenic butterfly

Seasonal generations of short-lived organisms often differ in their morphological, behavioural and life history traits, including body size. These differences may be either due to immediate effects of seasonally variable environment on organisms (responsive plasticity) or rely on presumably adaptive responses of organisms to cues signalizing forthcoming seasonal changes (anticipatory plasticity). When directly developing individuals of insects are larger than their overwintering conspecifics, the between-generation differences are typically ascribed to responsive plasticity in larval growth. We tested this hypothesis using the papilionid butterly Iphiclides podalirius as a model species. In laboratory experiments, we demonstrated that seasonal differences in food quality could not explain the observed size difference. Similarly, the size differences are not likely to be explained by the immediate effects of ambient temperature and photoperiod on larval growth. The qualitative pattern of natural size differences between the directly developing and diapausing butterflies could be reproduced in the laboratory as a response to photoperiod, indicating anticipatory character of the response. Directly developing and diapausing individuals followed an identical growth trajectory until the end of the last larval instar, with size differences appearing just a few days before pupation. Taken together, various lines of evidence suggest that between-generation size differences in I. podalirius are not caused by immediate effects of environmental factors on larval growth. Instead, these differences rather represent anticipatory plasticity and are thus likely to have an adaptive explanation. It remains currently unclear, whether the seasonal differences in adult size per se are adaptive, or if they constitute co-product of processes related to the diapause. Our study shows that it may be feasible to distinguish between different types of plasticity on the basis of empirical data even if fitness cannot be directly measured, and contributes to the emerging view about the predominantly adaptive nature of seasonal polyphenisms in insects.     

Effect of yeast culture on milk production and metabolic and reproductive performance of early lactation dairy cows

Background

The main objective of this study was to estimate the effect of supplementation with Saccaromyces cerevisiae (SC) (Yea-Sacc^® 1026) on milk production, metabolic parameters and the resumption of ovarian activity in early lactation dairy cows.

Methods

The experiment was conducted during 2005/2006 in a commercial tied-house farm with an average of 200 milking Estonian Holstein Friesian cows. The late pregnant multiparous cows (n = 46) were randomly divided into two groups; one group received 10 g yeast culture from two weeks before to 14 weeks after calving. The groups were fed a total mixed ration with silages and concentrates. Milk recording data and blood samples for plasma metabolites were taken. Resumption of luteal activity was determined using milk progesterone (P₄) measurements. Uterine bacteriology and ovarian ultrasonography (US) were performed and body condition scores (BCS) and clinical disease occurrences were recorded. For analysis, the statistical software Stata 9.2 and R were used to compute Cox proportional hazard and linear mixed models.

Results

The average milk production per cow did not differ between the groups (32.7 ± 6.4 vs 30.7 ± 5.3 kg/day in the SC and control groups respectively), but the production of milk fat (P < 0.001) and milk protein (P < 0.001) were higher in the SC group. There was no effect of treatment on BCS. The analysis of energy-related metabolites in early lactation showed no significant differences between the groups. In both groups higher levels of β-hydroxybutyrate (BHB) appeared from days 14 to 28 after parturition and the concentration of non-esterfied fatty acid (NEFA) was higher from days 1–7 post partum (PP). According to US and P₄ results, all cows in both groups ovulated during the experimental period. The resumption of ovarian activity (first ovulations) and time required for elimination of bacteria from the uterus did not differ between the groups.

Conclusion

Supplementation with SC had an effect on milk protein and fat production, but did not influence the milk yield. No effects on PP metabolic status, bacterial elimination from the uterus nor the resumption of ovarian activity were found.