Heritability and Inter-Population Differences in Lipid Profiles of \u3ci\u3eDrosophila melanogaster\u3c/i\u3e

Characterizing and understanding the complex spectrum of lipids in higher organisms lags far behind our analysis of genome and transcriptome sequences. Here we generate and evaluate comprehensive lipid profiles (\u3e200 lipids) of 92 inbred lines from five different Drosophila melanogaster populations. We find that the majority of lipid species are highly heritable, and even lipids with odd-chain fatty acids, which cannot be generated by the fly itself, also have high heritabilities. Abundance of the endosymbiont Wolbachia, a potential provider of odd-chained lipids, was positively correlated with this group of lipids. Additionally, we show that despite years of laboratory rearing on the same medium, the lipid profiles of the five geographic populations are sufficiently distinct for population discrimination. Our data predicts a strikingly different membrane fluidity for flies from the Netherlands, which is supported by their increased ethanol tolerance. We find that 18% of lipids show strong concentration differences between males and females. Through an analysis of the correlation structure of the lipid classes, we find modules of co-regulated lipids and begin to associate these with metabolic constraints. Our data provide a foundation for developing associations between variation in lipid composition with variation in other metabolic attributes, with genome-wide variation, and with metrics of health and overall reproductive fitness

Heritability and Inter-Population Differences in Lipid Profiles of <i>Drosophila melanogaster</i>

<div><p>Characterizing and understanding the complex spectrum of lipids in higher organisms lags far behind our analysis of genome and transcriptome sequences. Here we generate and evaluate comprehensive lipid profiles (>200 lipids) of 92 inbred lines from five different <i>Drosophila melanogaster</i> populations. We find that the majority of lipid species are highly heritable, and even lipids with odd-chain fatty acids, which cannot be generated by the fly itself, also have high heritabilities. Abundance of the endosymbiont <i>Wolbachia</i>, a potential provider of odd-chained lipids, was positively correlated with this group of lipids. Additionally, we show that despite years of laboratory rearing on the same medium, the lipid profiles of the five geographic populations are sufficiently distinct for population discrimination. Our data predicts a strikingly different membrane fluidity for flies from the Netherlands, which is supported by their increased ethanol tolerance. We find that 18% of lipids show strong concentration differences between males and females. Through an analysis of the correlation structure of the lipid classes, we find modules of co-regulated lipids and begin to associate these with metabolic constraints. Our data provide a foundation for developing associations between variation in lipid composition with variation in other metabolic attributes, with genome-wide variation, and with metrics of health and overall reproductive fitness.</p></div

Distribution of lipids and membrane fluidity.

<p>A: Proportion of total polar lipids comprised by each polar lipid class in the five populations, stratified by sex. B: Membrane fluidity index as determined by the PC/PE ratio for all populations and sexes. C: Ratio of unsaturated over saturated lipids grouped by lipid class, population and sex. A lipid class was only included if it contained saturated lipids. D: Log-transformed concentration of all lipid species in all lipid classes in males <i>vs</i>. females. Samples are color-coded by the number of double bonds and the FA length is partitioned into odd (x) and even (circle) groups.</p

ANOVA of lipid species by lipid class.

<p>ANOVA of lipid species by lipid class.</p

Netherlands flies have higher ethanol tolerance.

<p>Ethanol tolerance measured in duplicates for each sex in four lines from both the Netherlands and Tasmania. Red line indicates a survival rate of 0.5.</p

Odd-chain lipid concentration correlates with <i>Wolbachia</i> abundance.

<p>A: Fraction of odd-chained FAs estimated from the total carbon count per lipid species. Only lipid classes containing odd length FAs are included. B: Histogram of lipid species concentration correlation with normalized <i>Wolbachia</i> genome read depth (Spearman) for each fly line where <i>Wolbachia</i> was detected (<i>n</i> = 65). Lipid species are color-coded by lipid group and split by FA length categorized into odd and even.</p

Lipid network conforms with known metabolism and has high heritability.

<p>A: Metabolic network for the relations among lipid classes, as derived from the literature <a href="http://www.plosone.org/article/info:doi/10.1371/journal.pone.0072726#pone.0072726-Coleman1" target="_blank">[23]</a>. B: Network constructed from our lipid composition data using Cytoscape. All pairs of lipid classes with PCC >0.1 or PCC<−0.1 are connected in the network. A positive correlation between two lipid classes is represented by a green edge, while a negative correlation is represented by a red edge. The thickness of the edges is proportional to the magnitude of PCC between the lipid classes. C: Broad sense heritability (H²) for each measured lipid species grouped by lipid class. Circles are outliers and represent specific lipid species.</p

DAPC analysis reveals clear population separation in either males or females.

<p>A: Fraction of neutral lipids across population and sex. Value in brackets (cont.) identifies one FA of a total 2 for DAGs and a total 3 for TAGs. B: DAPC analysis for all flies investigating the sex separation. Inset shows the total variance explained by the PCos. Retained PCos are colored black. C and D: DAPC analysis for males (C) and females (D) separating the 5 populations. Colored crosses and their connections show the minimum-spanning tree based on the population distances. Df = Discriminant function. Inset as in B. E: Percent of individuals that are assigned to their biological population using the DAPC of C and D. F: Leave-one-out approach testing the robustness of the population assignment from the DAPC analysis in C and D. G: Eigenvectors from the male DAPC (C) are applied to the female lipid dataset, and it was determined how well this allows for population separation by measuring the re-assignment of individuals to their biological population. H: Same as F, but female derived eigenvectors are applied to the male dataset.</p

MMC clustering reveals distinct clusters only in female lipid data.

<p>A and B: MMC matrix for male (A) and female (B) lipid concentration with any population effect removed. C: Lipid class distribution across identified clusters in females (from B). D: Odd and even chain FA distribution across the same clusters.</p