Brandon S. Cooper

Revisiting classic clines in Drosophila melanogaster in the age of genomics

Adaptation to spatially varying environments has been studied for decades, but advances in sequencing technology are now enabling researchers to investigate the landscape of genetic variation underlying this adaptation genome wide. In this review we highlight some of the decades-long research on local adaptation in Drosophila melanogaster from well-studied clines in North America and Australia. We explore the evidence for parallel adaptation and identify commonalities in the genes responding to clinal selection across continents as well as discussing instances where patterns differ among clines. We also investigate recent studies utilizing whole-genome data to identify clines in D. melanogaster and several other systems. Although connecting segregating genomic variation to variation in phenotypes and fitness remains challenging, clinal genomics is poised to increase our understanding of local adaptation and the selective pressures that drive the extensive phenotypic diversity observed in nature.

In a variable thermal environment selection favors greater plasticity of cell membranes in Drosophila melanogaster.

Theory predicts that developmental plasticity, the capacity to change phenotypic trajectory during development, should evolve when the environment varies sufficiently among generations, owing to temporal (e.g., seasonal) variation or to migration among environments. We characterized the levels of cellular plasticity during development in populations of Drosophila melanogaster experimentally evolved for over three years in either constant or temporally variable thermal environments. We used two measures of the lipid composition of cell membranes as indices of physiological plasticity (a.k.a. acclimation): (1) change in the ratio of phosphatidylethanolamine (PE) to phosphatidylcholine (PC) and (2) change in lipid saturation (number of double bonds) in cool (16°C) relative to warm (25°C) developmental conditions. Flies evolved under variable environments had a greater capacity to acclimate the PE/PC ratio compared to flies evolved in constant environments, supporting the prediction that environments with high among‐generation variance favor greater developmental plasticity. Our results are consistent with the selective advantage of a more environmentally sensitive allele that may have associated costs in constant environments.

Profiling and quantification of Drosophila melanogaster lipids using liquid chromatography/mass spectrometry

We present here the findings of global profiling of Drosophila lipids using liquid chromatography/tandem mass spectrometry (LC/MS/MS) on an LTQ-Orbitrap instrument. In addition, we present a multiple reaction monitoring (LC-MRM) method for the absolute quantification of the major phosphatidylethanolamine (PE) and phosphatidylcholine (PC) lipids of Drosophila. Using both normal- and reversed-phase LC followed by accurate mass analysis and MS/MS on an LTQ-Orbitrap instrument, we evaluated the lipid composition of the fruit fly Drosophila melanogaster. A total of 74 lipid species were identified consisting of glycerphospholipids belonging to the PE, PC, phosphatidylglycerol (PG), phosphatidylinositol (PI) and phosphatidylserine (PS) classes including several plasmanyl PE species, as well as triacylglycerides, cardiolipins, ceramides, and PE ceramides. Individual PE and PC phospholipids were then quantified using an LC-MRM approach. Reversed-phase chromatography followed by monitoring on a QTrap 4000 instrument of 21 MRM transitions combined with calibration curves constructed using internal standards enabled the absolute quantification of 28 PE and PC lipid species with limits of quantification of 3 and 5 pg/μL, respectively. Internal standards accounted for the differences in ionization efficiencies of PE and PC phospholipids, facilitating more accurate lipid abundance measurements. The method presented here builds on previous Drosophila work by making the quantification of absolute lipid abundance possible and will be of interest to scientists who study variation and changes in the degree of unsaturation, fatty acid carbon length, and head-group concentration among individuals of different genotypes in response to environmental, genetic, or physiological perturbation in small insects. It will also be particularly useful to biologists interested in adaptation and acclimation of cellular membranes in response to thermal heterogeneity.

Isopods Failed to Acclimate Their Thermal Sensitivity of Locomotor Performance during Predictable or Stochastic Cooling

Most organisms experience environments that vary continuously over time, yet researchers generally study phenotypic responses to abrupt and sustained changes in environmental conditions. Gradual environmental changes, whether predictable or stochastic, might affect organisms differently than do abrupt changes. To explore this possibility, we exposed terrestrial isopods (Porcellio scaber) collected from a highly seasonal environment to four thermal treatments: (1) a constant 20°C; (2) a constant 10°C; (3) a steady decline from 20° to 10°C; and (4) a stochastic decline from 20° to 10°C that mimicked natural conditions during autumn. After 45 days, we measured thermal sensitivities of running speed and thermal tolerances (critical thermal maximum and chill-coma recovery time). Contrary to our expectation, thermal treatments did not affect the thermal sensitivity of locomotion; isopods from all treatments ran fastest at 33° to 34°C and achieved more than 80% of their maximal speed over a range of 10° to 11°C. Isopods exposed to a stochastic decline in temperature tolerated cold the best, and isopods exposed to a constant temperature of 20°C tolerated cold the worst. No significant variation in heat tolerance was observed among groups. Therefore, thermal sensitivity and heat tolerance failed to acclimate to any type of thermal change, whereas cold tolerance acclimated more during stochastic change than it did during abrupt change.

Similar Efficacies of Selection Shape Mitochondrial and Nuclear Genes in Both Drosophila melanogaster and Homo sapiens.

Deleterious mutations contribute to polymorphism even when selection effectively prevents their fixation. The efficacy of selection in removing deleterious mitochondrial mutations from populations depends on the effective population size (Ne) of the mitochondrial DNA and the degree to which a lack of recombination magnifies the effects of linked selection. Using complete mitochondrial genomes from Drosophila melanogaster and nuclear data available from the same samples, we reexamine the hypothesis that nonrecombining animal mitochondrial DNA harbor an excess of deleterious polymorphisms relative to the nuclear genome. We find no evidence of recombination in the mitochondrial genome, and the much-reduced level of mitochondrial synonymous polymorphism relative to nuclear genes is consistent with a reduction in Ne. Nevertheless, we find that the neutrality index, a measure of the excess of nonsynonymous polymorphism relative to the neutral expectation, is only weakly significantly different between mitochondrial and nuclear loci. This difference is likely the result of the larger proportion of beneficial mutations in X-linked relative to autosomal loci, and we find little to no difference between mitochondrial and autosomal neutrality indices. Reanalysis of published data from Homo sapiens reveals a similar lack of a difference between the two genomes, although previous studies have suggested a strong difference in both species. Thus, despite a smaller Ne, mitochondrial loci of both flies and humans appear to experience similar efficacies of purifying selection as do loci in the recombining nuclear genome.

Wolbachia in the Drosophila yakuba Complex: Pervasive Frequency Variation and Weak Cytoplasmic Incompatibility, but No Apparent Effect on Reproductive Isolation

Three hybridizing species—the clade [(Drosophila yakuba, D. santomea), D. teissieri]—comprise the yakuba complex in the D. melanogaster subgroup. Their ranges overlap on Bioko and São Tomé, islands off west Africa. All three species are infected with Wolbachia—maternally inherited, endosymbiotic bacteria, best known for manipulating host reproduction to favor infected females. Previous analyses reported no cytoplasmic incompatibility (CI) in these species. However, we discovered that Wolbachia from each species cause intraspecific and interspecific CI. In D. teissieri, analyses of F1 and backcross genotypes show that both host genotype and Wolbachia variation modulate CI intensity. Wolbachia-infected females seem largely protected from intraspecific and interspecific CI, irrespective of Wolbachia and host genotypes. Wolbachia do not affect host mating behavior or female fecundity, within or between species. The latter suggests little apparent effect of Wolbachia on premating or gametic reproductive isolation (RI) between host species. In nature, Wolbachia frequencies varied spatially for D. yakuba in 2009, with 76% (N = 155) infected on São Tomé, and only 3% (N = 36) infected on Bioko; frequencies also varied temporally in D. yakuba and D. santomea on São Tomé between 2009 and 2015. These temporal frequency fluctuations could generate asymmetries in interspecific mating success, and contribute to postzygotic RI. However, the fluctuations in Wolbachia frequencies that we observe also suggest that asymmetries are unlikely to persist. Finally, we address theoretical questions that our empirical findings raise about Wolbachia persistence when conditions fluctuate, and about the stable coexistence of Wolbachia and host variants that modulate Wolbachia effects.

Statistical Confusion Among Graduate Students: Sickness or Symptom?

Abstract Statistics is one of the most important yet difficult subjects for many ecology and wildlife graduate students to learn. Insufficient knowledge about how to conduct quality science and the ongoing debate about the relative value of competing statistical ideologies contribute to uncertainties among graduate students regarding which statistical tests are most appropriate. Herein, we argue that increased education of the available statistical tests alone is unlikely to ameliorate the problem. Instead, we suggest that statistical uncertainties among graduate students are a secondary symptom of a larger problem. We believe the root cause lies in the lack of education on how to conduct science as an integrated process from hypothesis creation through statistical analysis. We argue that if students are taught to think about how each step of the process will affect all other steps, many statistical uncertainties will be avoided.