From whole bodies to single cells: A guide to transcriptomic approaches for ecology and evolutionary biology.

RNA sequencing (RNAseq) methodology has experienced a burst of technological developments in the last decade, which has opened up opportunities for studying the mechanisms of adaptation to environmental factors at both the organismal and cellular level. Selecting the most suitable experimental approach for specific research questions and model systems can, however, be a challenge and researchers in ecology and evolution are commonly faced with the choice of whether to study gene expression variation in whole bodies, specific tissues, and/or single cells. A wide range of sometimes polarised opinions exists over which approach is best. Here, we highlight the advantages and disadvantages of each of these approaches to provide a guide to help researchers make informed decisions and maximise the power of their study. Using illustrative examples of various ecological and evolutionary research questions, we guide the readers through the different RNAseq approaches and help them identify the most suitable design for their own projects.

Systematic approaches to assessing high-temperature limits to fertility in animals.

Critical thermal limits (CTLs) gauge the physiological impact of temperature on survival or critical biological function, aiding predictions of species range shifts and climatic resilience. Two recent Drosophila species studies, using similar approaches to determine temperatures that induce sterility (thermal fertility limits [TFLs]), reveal that TFLs are often lower than CTLs and that TFLs better predict both current species distributions and extinction probability. Moreover, many studies show fertility is more sensitive at less extreme temperatures than survival (thermal sensitivity of fertility [TSF]). These results present a more pessimistic outlook on the consequences of climate change. However, unlike CTLs, TFL data are limited to Drosophila, and variability in TSF methods poses challenges in predicting species responses to increasing temperature. To address these data and methodological gaps, we propose 3 standardized approaches for assessing thermal impacts on fertility. We focus on adult obligate sexual terrestrial invertebrates but also provide modifications for other animal groups and life-history stages. We first outline a "gold-standard" protocol for determining TFLs, focussing on the effects of short-term heat shocks and simulating more frequent extreme heat events predicted by climate models. As this approach may be difficult to apply to some organisms, we then provide a standardized TSF protocol. Finally, we provide a framework to quantify fertility loss in response to extreme heat events in nature, given the limitations in laboratory approaches. Applying these standardized approaches across many taxa, similar to CTLs, will allow robust tests of the impact of fertility loss on species responses to increasing temperatures.

Developmental heat stress interrupts spermatogenesis inducing early male sterility in Drosophila melanogaster.

Thermal stress leads to fertility reduction, can cause temporal sterility and thus results in fitness loss with severe ecological and evolutionary consequences, e.g., threatening species persistence already at sub-lethal temperatures. For males we here tested which developmental stage is particularly sensitive to heat stress in the model species Drosophila melanogaster. As developmental stages characterize the different steps of sperm development, we could narrow down which particular processes are heat sensitive. We studied early male reproductive ability and, by following recovery dynamics after a move to benign temperatures, we investigated general mechanisms behind a subsequent gain of fertility. We found strong support to suggest that the last steps of spermatogenesis are particularly sensitive to heat stress, as processes occurring during the pupal stage were mostly interrupted, delaying both sperm production and sperm maturation. Moreover, further measurements in the testes and for proxies of sperm availability indicating the onset of adult reproductive capacity matched the expected heat-induced delay in completing spermatogenesis. We discuss these results within the context of how heat stress affects reproductive organ function and the consequences for male reproductive potential.

Recovery from heat-induced infertility-A study of reproductive tissue responses and fitness consequences in male Drosophila melanogaster.

The predicted temperature increase caused by climate change is a threat to biodiversity. Across animal taxa, male reproduction is often sensitive to elevated temperatures leading to fertility loss, and in more adverse scenarios, this can result in sterility when males reach their upper thermal fertility limit. Here, we investigate temperature-induced changes in reproductive tissues, fertility reduction, sterility, and the associated fitness loss during the subsequent recovery phase in male Drosophila melanogaster. We heat-stressed males during development and either allowed them to recover or not in early adulthood while measuring several determinants of male reproductive success. We found significant differences in recovery rate, organ sizes, sperm production, and other key reproductive traits among males from our different temperature treatments. Sperm maturation was impaired before reaching the upper thermal sterility threshold. While some effects were reversible, this did not compensate for the fitness loss due to damage imposed during development. Surprisingly, developmental heat stress was damaging to accessory gland growth, and female post-mating responses mediated by seminal fluid proteins were impaired regardless of the possibility of recovery. We suggest that sub-lethal thermal sterility and the subsequent fertility reduction are caused by a combination of inefficient functionality of both the accessory gland and testes.

Reproductive Ecology of Drosophila obscura: A Cold Adapted Species.

The study of insect reproductive ecology is essential to determine species distributions and fate under changing environments. Species adapted to harsh environments are good examples to investigate the reproductive mechanisms that allow them to cope with the challenging conditions. We here focus on studying for the first time the reproductive ecology of a cold-adapted Drosophila obscura (Diptera: Drosophilidae) strain collected in Finland (subarctic climate region). We tested several reproductive traits such as fertility and fecundity to observe the onset of reproduction and gauge when sexual maturity is reached in both males and females. We combined these measures with an analysis of changes of their reproductive organs shortly after eclosion. We found that males matured several days before females and that this process was underpinned by female egg maturation and male accessory gland growth, while sperm was already present in two-day old males. This delayed maturation is not observed to the same extent in other closely related species and might be a signature of exposure to harsh environments. Whether this delay is an adaptation to cope with variation in resource availability or prolonged unfavorable temperatures is though not clear. Finally, our study adds to the set of reproductive mechanisms used by cold adapted species and the information presented here contributes to understanding the breadth of Drosophila reproductive ecology.

Sex peptide receipt alters macronutrient utilization but not optimal yeast-sugar ratio in Drosophila melanogaster females.

Upon mating, females alter a multitude of physiological and morphological traits to accommodate the demands of reproduction. Changes not only include reproductive tissues but also non-reproductive tissues. For example, in Drosophila melanogaster the gut increases in circumference after mating, likely to facilitate a higher absorption and provision of macronutrients to maturing eggs. A male ejaculatory protein, the sex peptide, is instrumental to mediating several post-mating changes and receipt increases nutrient uptake as well as shifts taste preferences in mated females. We here tested whether sex peptide receipt also alters the protein: carbohydrate ratio at which females maximize their fitness. To test this, we mated females to males lacking sex peptide or control males and fed them with known volumes and concentrations of sugar and yeast. This enabled us to determine how the sugar to yeast ratio affects lifetime egg output as well as lifespan of females mated to the two male types. Sex peptide did not shift the optimal ratio. Instead, sex peptide receipt aided females in increasing their egg output at low macronutrient concentrations, but this advantage disappeared at higher macronutrient intake rates. Assuming that nutrient limitation might be common, then receipt of SP is beneficial under poor conditions.

Genotypes and their interaction effects on reproduction and mating-induced immune activation in Drosophila melanogaster.

Mating causes considerable alterations in female physiology and behaviour, and immune gene expression, partly due to proteins transferred from males to females during copulation. The magnitude of these phenotypic changes could be driven by the genotypes of males and females, as well as their interaction. To test this, we carried out a series of genotype-by-genotype (G × G) experiments using Drosophila melanogaster populations from two distant geographical locations. We expected lines to have diverged in male reproductive traits and females to differ in their responses to these traits. We examined female physiological and behavioural post-mating responses to male mating traits, that is behaviour and ejaculate composition, in the short to mid-term (48 hr) following mating. We then explored whether a sexually transferred molecule, sex peptide (SP), is the mechanism behind our observed female post-mating responses. Our results show that the genotypes of both sexes as well as the interaction between male and female genotypes affect mating and post-mating reproductive traits. Immune gene expression of three candidate genes increased in response to mating and was genotype-dependent but did not show a G × G signature. Males showed genotype-dependent SP expression in the 7 days following eclosion, but female genotypes showed no differential sensitivity to the receipt of SP. The two genotypes demonstrated clear divergence in physiological traits in short- to mid-term responses to mating, but the longer-term consequences of these initial dynamics remain to be uncovered.

Male reproductive ageing: a tale of the whole ejaculate.

Ageing is nearly ubiquitous and encompasses all biological functions. We here focus on age-dependent changes in male reproductive capacity across a broad range of animal taxa. While there has been a long-standing focus on mating ability and overall reproductive success, we here highlight the underlying mechanisms that explain loss in fertilisation capacity in ageing males. Fertilisation is mediated by not only the presence of sperm, but also the cocktail of seminal fluid proteins that ensure sperm survival, capacitation and interaction with female physiology. Sperm ageing has received much attention in studies of male reproductive senescence; however, post-mating processes include a number of interlocked steps that together cumulate in successful fertilisation. As such we consider male ability to elicit female post mating responses such as uterine conformational changes, sperm storage and ovulation and the components within the ejaculate that mediate these post-mating processes. For the latter seminal fluid proteins are key and hence we reflect on age-dependent changes in quality of the entire ejaculate and its consequences for male reproductive capacity. While first studies accrue and highlight that changes in the non-sperm fraction can explain substantial variation in senescent male reproductive success and male ability to induce post-mating responses necessary for fertilisation many open questions still remain that warrant further investigations. One being what the potential age-dependent changes in composition are or whether there is a general decline and how this interacts with sperm to affect fertilisation success. Further, the impact females might have to ameliorate these changes will be an area of interest.

Sexual conflict drives male manipulation of female postmating responses in Drosophila melanogaster.

In many animals, females respond to mating with changes in physiology and behavior that are triggered by molecules transferred by males during mating. In Drosophila melanogaster, proteins in the seminal fluid are responsible for important female postmating responses, including temporal changes in egg production, elevated feeding rates and activity levels, reduced sexual receptivity, and activation of the immune system. It is unclear to what extent these changes are mutually beneficial to females and males or instead represent male manipulation. Here we use an experimental evolution approach in which females are randomly paired with a single male each generation, eliminating any opportunity for competition for mates or mate choice and thereby aligning the evolutionary interests of the sexes. After >150 generations of evolution, males from monogamous populations elicited a weaker postmating stimulation of egg production and activity than males from control populations that evolved with a polygamous mating system. Males from monogamous populations did not differ from males from polygamous populations in their ability to induce refractoriness to remating in females, but they were inferior to polygamous males in sperm competition. Mating-responsive genes in both the female abdomen and head showed a dampened response to mating with males from monogamous populations. Males from monogamous populations also exhibited lower expression of genes encoding seminal fluid proteins, which mediate the female response to mating. Together, these results demonstrate that the female postmating response, and the male molecules involved in eliciting this response, are shaped by ongoing sexual conflict.

Physiological Maturation Lags Behind Behavioral Maturation in Newly Eclosed Drosophila melanogaster Males.

The accessory gland (AG) produces seminal fluid proteins that are transferred to the female upon mating in many insects. These seminal fluid proteins often promote a male's post-copulatory reproductive success. Despite its crucial function many males eclose with a small gland not yet containing the full set of proteins. Thus, they need a physiological maturation period. Using Drosophila melanogaster, we tested whether this physiological maturation is linked to behavioral maturation in males and to what extent seminal fluid allocation patterns are influenced by physiological maturation. To that end, we measured AG protein content (as a proxy for physiological maturation) of young, immature males that were either successful in gaining a mating, but prevented from transferring seminal fluid proteins, or unsuccessful, thus using mating success as a proxy for behavioral maturation. Furthermore, we compared ejaculate allocation in immature and mature males in a single mating. Though mating success and gland maturation increase with male age, we found no evidence for a fine-tuned synchronization of behavioral and physiological maturation in males. This is especially surprising since we found reduced ejaculate allocation in very young, immature males, hinting at reduced fitness benefits from early matings in D. melanogaster.

The effect of mating history on male reproductive ageing in Drosophila melanogaster.

Mating bears costs, but how these costs affect the senescence of reproductive traits in males has received relatively little attention. Males of many species show reduced benefits from pre- and post-copulatory reproductive traits during ageing. Senescence of post-copulatory reproductive traits is often linked to a reduction in sperm quantity and quality, but can also be a consequence of changes in seminal fluid proteins that are transferred alongside sperm during mating. Here we investigated how mating history affects male reproductive ageing, especially at the post-copulatory level, using Drosophila melanogaster, a species in which links between seminal fluid proteins and male reproductive traits are well established. Besides a male cohort kept virgin until the start of the experiment we also included a cohort of males kept together with females allowing for ample mating opportunities. With these males we conducted a series of behavioral experiments covering several aspects of male reproductive success with males ranging in age from 4 days to 6 weeks after eclosion. Additionally, we investigated the storage capacity of male accessory glands (AG), the production site of the majority of seminal fluid proteins. We found male reproductive success to decline with increasing male age and, most importantly, males with prior matings showed a reduced performance in pre-copulatory success. However, our data suggest a constant short-term cost of mating rather than an accelerated senescence of pre-copulatory traits. In contrast, senescence of post-copulatory reproductive traits differed between mated and virgin males, hinting at mating costs in males altering the ageing process. We could not find any differences in the capacity of the AG to store seminal fluid proteins, however, our data suggest that old males transfer fewer seminal fluid proteins in a single mating. We conclude that a variety of traits is affected by male reproductive ageing in D. melanogaster with the cost of mating varying in its impact on senescence in these traits.

Divergence in sex peptide-mediated female post-mating responses in Drosophila melanogaster.

Transfer and receipt of seminal fluid proteins crucially affect reproductive processes in animals. Evolution in these male ejaculatory proteins is explained with post-mating sexual selection, but we lack a good understanding of the evolution of female post-mating responses (PMRs) to these proteins. Some of these proteins are expected to mediate sexually antagonistic coevolution generating the expectation that females evolve resistance. One candidate in Drosophila melanogaster is the sex peptide (SP) which confers cost of mating in females. In this paper, we compared female SP-induced PMRs across three D. melanogaster wild-type populations after mating with SP-lacking versus control males including fitness measures. Surprisingly, we did not find any evidence for SP-mediated fitness costs in any of the populations. However, female lifetime reproductive success and lifespan were differently affected by SP receipt indicating that female PMRs diverged among populations. Injection of synthetic SP into virgin females further supported these findings and suggests that females from different populations require different amounts of SP to effectively initiate PMRs. Molecular analyses of the SP receptor suggest that genetic differences might explain the observed phenotypical divergence. We discuss the evolutionary processes that might have caused this divergence in female PMRs.

The impact of ageing on male reproductive success in Drosophila melanogaster.

Male reproductive ageing has been mainly explained by a reduction in sperm quality with negative effects on offspring development and quality. In addition to sperm, males transfer seminal fluid proteins (Sfps) at mating; Sfps are important determinants of male reproductive success. Receipt of Sfps leads to female post-mating changes including physiological changes, and affects sperm competition dynamics. Using the fruit fly Drosophila melanogaster we studied ageing males' ability to induce female post-mating responses and determined the consequences of male ageing on their reproductive success. We aged males for up to 7weeks and assayed their ability to: i) gain a mating, ii) induce egg-laying and produce offspring, iii) prevent females from remating and iv) transfer sperm and elicit storage after a single mating. We found that with increasing age, males were less able to induce post-mating responses in their mates; moreover ageing had negative consequences for male success in competitive situations. Our findings indicate that with advancing age male flies transferred less effective ejaculates and that Sfp composition might change over a male's lifetime in quantity and/or quality, significantly affecting his reproductive success.

Precopulatory but not postcopulatory male reproductive traits diverge in response to mating system manipulation in Drosophila melanogaster.

Competition between males creates potential for pre- and postcopulatory sexual selection and conflict. Theory predicts that males facing risk of sperm competition should evolve traits to secure their reproductive success. If those traits are costly to females, the evolution of such traits may also increase conflict between the sexes. Conversely, under the absence of sperm competition, one expectation is for selection on male competitive traits to relax thereby also relaxing sexual conflict. Experimental evolution studies are a powerful tool to test this expectation. Studies in multiple insect species have yielded mixed and partially conflicting results. In this study, we evaluated male competitive traits and male effects on female costs of mating in Drosophila melanogaster after replicate lines evolved for more than 50 generations either under enforced monogamy or sustained polygamy, thus manipulating the extent of intrasexual competition between males. We found that in a setting where males competed directly with a rival male for access to a female and fertilization of her ova polygamous males had superior reproductive success compared to monogamous males. When comparing reproductive success solely in double mating standard sperm competition assays, however, we found no difference in male sperm defense competitiveness between the different selection regimes. Instead, we found monogamous males to be inferior in precopulatory competition, which indicates that in our system, enforced monogamy relaxed selection on traits important in precopulatory rather than postcopulatory competition. We discuss our findings in the context of findings from previous experimental evolution studies in Drosophila ssp. and other invertebrate species.

Gene expression changes in male accessory glands during ageing are accompanied by reproductive decline in Drosophila melanogaster.

Senescence is accompanied by loss of reproductive functions. Here, we studied reproductive ageing in Drosophila melanogaster males and asked whether the expected decline in male reproductive success is due to diminished functionality of the male accessory gland (AG). The male AG produces the majority of seminal fluid proteins (SFPs) transferred to the female at mating. SFPs induce female postmating changes and are key to male reproductive success. We measured age-dependent gene expression changes for five representative SFP genes in males from four different age groups ranging from 1 to 6 weeks after eclosion. Simultaneously, we also measured male reproductive success in postmating traits mediated by transfer of these five SFPs. We found a decreased in male SFP gene expression with advancing age and an accompanying decline in male postmating success. Hence, male reproductive senescence is associated with a decline in functionality of the male AG. While overall individual SFP genes decreased in expression, our results point towards the idea that the composition of an ejaculate might change with male age as the rate of change was variable for those five genes.

Sexual conflict over remating interval is modulated by the sex peptide pathway.

Sexual conflict, in which the evolutionary interests of males and females diverge, shapes the evolution of reproductive systems across diverse taxa. Here, we used the fruit fly to study sexual conflict in natural, three-way interactions comprising a female, her current and previous mates. We manipulated the potential for sexual conflict by using sex peptide receptor (SPR) null females and by varying remating from 3 to 48 h, a period during which natural rematings frequently occur. SPR-lacking females do not respond to sex peptide (SP) transferred during mating and maintain virgin levels of high receptivity and low fecundity. In the absence of SPR, there was a convergence of fitness interests, with all individuals gaining highest productivity at 5 h remating. This suggests that the expression of sexual conflict was reduced. We observed an unexpected second male-specific advantage to early remating, resulting from an increase in the efficiency of second male sperm use. This early window of opportunity for exploitation by second males depended on the presence of SPR The results suggest that the SP pathway can modulate the expression of sexual conflict in this system, and show how variation in the selective forces that shape conflict and cooperation can be maintained.

Effect of competitive cues on reproductive morphology and behavioral plasticity in male fruitflies.

Phenotypic plasticity will be favored whenever there are significant fitness benefits of responding to environmental variation. The extent and nature of the plasticity that evolves depends on the rate of environmental fluctuations and the capacity to track and respond to that variability. Reproductive environments represent one arena in which changes can be rapid. The finding that males of many species show morphological, physiological, and behavioral plasticity in response to premating and postmating reproductive competition (RC) suggests that plasticity is broadly beneficial. The developmental environment is expected to accurately predict the average population level of RC but to be a relatively poor indicator of immediate RC at any particular mating. Therefore, we predict that manipulation of average RC during development should cause a response in plasticity "set" during development (e.g., size of adult reproductive structures), but not in flexible plasticity determined by the immediate adult environment (e.g., behavioral plasticity in mating duration). We tested this prediction in Drosophila melanogaster males by manipulating 2 independent cues of average RC during development: 1) larval density and 2) the presence or absence of adult males within larval culture vials. Consistent with the prediction, both manipulations resulted in the development of males with significantly larger adult accessory glands (although testis size decreased when males were added to culture vials). There was no effect on adult plasticity (mating duration, extended mating in response to rivals). The results suggest that males have evolved independent responses to long- and short-term variation in RC.

A screen for bacterial endosymbionts in the model organisms Tribolium castaneum, T. confusum, Callosobruchus maculatus, and related species.

Reproductive parasites such as Wolbachia are extremely widespread amongst the arthropods and can have a large influence over the reproduction and fitness of their hosts. Undetected infections could thus confound the results of a wide range of studies that focus on aspects of host behavior, reproduction, fitness, and degrees of reproductive isolation. This potential problem has already been underlined by work investigating the incidence of Wolbachia infections in stocks of the model system Drosophila melanogaster. Here we survey a range of lab stocks of further commonly used model arthropods, focusing especially on the flour beetles Tribolium castaneum and Tribolium confusum, the cowpea weevil Callosobruchus maculatus and related species (Coleoptera: Tenebrionidae and Bruchidae). These species are widespread stored product pests so knowledge of infections with symbionts further has potential use in informing biocontrol measures. Beetles were assessed for infection with 3 known microbial reproductive parasites: Wolbachia, Rickettsia, Spiroplasma. Infections with some of these microbes were found in some of the lab stocks studied, although overall infections were relatively rare. The consequences of finding infections in these or other species and the type of previous studies likely to be affected most are discussed.

Prior mating success can affect allocation towards future sexual signaling in crickets.

Fitness is often correlated with the expression level of a sexually selected trait. However, sexually selected traits are costly to express such that investment in their expression should be optimised to maximize their overall fitness gains. Social interactions, in the form of successful and unsuccessful matings, may offer males one type of feedback allowing them to gauge how to allocate their resources towards sexual signaling. Here we tested whether adult male black field crickets (Teleogryllus commodus) modify the extent of their calling effort (the sexually selected trait) in response to successful and unsuccessful matings with females. To examine the effect that mating interactions with females have on investment into sexual signaling, we monitored male calling effort after maturation and then provided males with a female at two points within their life, manipulating whether or not males were able to successfully mate each time. Our results demonstrate that males alter their investment towards sexual signaling in response to successful matings, but only if the experience occurs early in their life. Males that mated early decreased their calling effort sooner than males that were denied a mating. Our results demonstrate that social feedback in the form of successful and unsuccessful matings has the potential to alter the effort a male places towards sexual signaling.

MicroRNAs influence reproductive responses by females to male sex peptide in Drosophila melanogaster.

Across taxa, female behavior and physiology change significantly following the receipt of ejaculate molecules during mating. For example, receipt of sex peptide (SP) in female Drosophila melanogaster significantly alters female receptivity, egg production, lifespan, hormone levels, immunity, sleep, and feeding patterns. These changes are underpinned by distinct tissue- and time-specific changes in diverse sets of mRNAs. However, little is yet known about the regulation of these gene expression changes, and hence the potential role of microRNAs (miRNAs), in female postmating responses. A preliminary screen of genomic responses in females to receipt of SP suggested that there were changes in the expression of several miRNAs. Here we tested directly whether females lacking four of the candidate miRNAs highlighted (miR-279, miR-317, miR-278, and miR-184) showed altered fecundity, receptivity, and lifespan responses to receipt of SP, when mated once or continually to SP null or control males. The results showed that miRNA-lacking females mated to SP null males exhibited altered receptivity, but not reproductive output, in comparison to controls. However, these effects interacted significantly with the genetic background of the miRNA-lacking females. No significant survival effects were observed in miRNA-lacking females housed continually with SP null or control males. However, continual exposure to control males that transferred SP resulted in significantly higher variation in miRNA-lacking female lifespan than did continual exposure to SP null males. The results provide the first insight into the effects and importance of miRNAs in regulating postmating responses in females.