Using single‐cell genomics to understand developmental processes and cell fate decisions

High‐throughput ‐omics techniques have revolutionised biology, allowing for thorough and unbiased characterisation of the molecular states of biological systems. However, cellular decision‐making is inherently a unicellular process to which “bulk” ‐omics techniques are poorly suited, as they capture ensemble averages of cell states. Recently developed single‐cell methods bridge this gap, allowing high‐throughput molecular surveys of individual cells. In this review, we cover core concepts of analysis of single‐cell gene expression data and highlight areas of developmental biology where single‐cell techniques have made important contributions. These include understanding of cell‐to‐cell heterogeneity, the tracing of differentiation pathways, quantification of gene expression from specific alleles, and the future directions of cell lineage tracing and spatial gene expression analysis.     

Sex-specific effects of developmental environment on reproductive trait expression in Drosophila melanogaster

Variation in the expression of reproductive traits provides the raw material upon which sexual selection can act. It is therefore important to understand how key factors such as environmental variation influence the expression of reproductive traits, as these will have a fundamental effect on the evolution of mating systems. It is also important to consider the effects of environmental variation upon reproductive traits in both sexes and to make comparisons with the environment to which the organism is adapted. In this study, we addressed these issues in a systematic study of the effect of a key environmental factor, variation in larval density, on reproductive trait expression in male and female Drosophila melanogaster. To do this, we compared reproductive trait expression when flies were reared under controlled conditions at eight different larval densities that covered a 20-fold range. Then, to place these results in a relevant context, we compared the results to those from flies sourced directly from stock cages. Many reproductive traits were surprisingly insensitive to variation in larval density. A notable exception was nonlinear variation in female fecundity. In contrast, we found much bigger differences in comparisons with flies from stock cages-including differences in body size, latency to mate, copulation duration, fecundity, and male share of paternity in a competitive environment. For a number of traits, even densities of 1000 larvae per vial (125 larvae per mL of food) did not phenocopy stock cage individuals. This study reveals novel patterns of sex-specific sensitivity to environmental variation that will influence the strength of sexual selection. It also illustrates the importance of comparisons with the environment to which individuals are adapted.     

Temperature and growth in Carcinus maenas L. (Decapoda: Portunidae) larvae reared in the laboratory from hatching through metamorphosis

Larvae of Carcinus maenas L. were reared in the laboratory from hatching through metamorphosis at 9, 12, and 18°C. Dry weight (DW) and elemental contents of carbon (C), nitrogen (N), and hydrogen (H) were analysed at short intervals through successive larval moulting cycles (four zoea-stages, megalopa), and newly metamorphosed crabs. C. maenas larvae grew significantly during all instars, at all temperatures tested. Biomass (DW, C, N, H) and energy (Joule) slightly declined shortly before ecdysis in zoea stages. This terminal decrease was more distinct in the megalopa stage, where ≈39 and 83% of the maximum energy attained, was lost at 12 and 18°C, respectively. Changes of biomass and energy in successive moult cycles showed best fits to quadratic equations, whereas their maximum in successive larval instars formed exponential sequences with time. Due to parabolic growth curves, biomass and energy accumulation within single instars were discussed as maximum (MG) and effective growth (EG), considering gain both at times of maximum biomass, and shortly before ecdysis. Metamorphosing larvae achieved EG with 1137% (DW), 1195% (C), 1108% (N), 1395% (H), 1339% (Joule) at 12°C, and 1140% (DW), 1099% (C), 1133% (N), 1225% (H), 1107% (Joule) at 18°C, relative to newly hatched zoea-1. Ash content and inorganic C in newly hatched zoea-1, were 29.4% and 5.5% ash, respectively. The stoichiometric C H N method of Gnaiger & Bitterlich was used to assess protein, lipid, and carbohydrate compositions. Obviously proteins formed the major part of larval biomass (>50% DW). C: N ratios indicate that more lipid than protein was built up shortly after moulting, but relatively more protein was subsequently accumulated. Temperature effects on larval growth (MG, EG), growth rates (GR), and gross growth efficiencies (K₁) were discussed. C. maenas zoea stages accumulated energy and biomass with higher efficiencies at 18 than at 12°C. Megalopa growth seemed to be limited at 18°C, showing lower K₁ values than at 12°C. N was accumulated with higher efficiencies than C in all larval stages. Characteristic variations in larval K₁ values between premoult and ecdysis were discussed. Cumulative gross growth efficiencies (MG-related) were calculated as ≈11 and 10%, at 12 and 18°C, respectively.