Mechanisms for the environmental regulation of gene expression: ecological aspects of animal development

Heritability in the Rhesus Macaque (Macaca mulatta) Vertebral Column

The vertebral column plays a central role in primate locomotion and positional behavior. Understanding its evolution, therefore, has the potential to clarify evolutionary processes that have occurred in the primate lineage as well as the specific behaviors of extinct primates. However, to understand primate vertebral anatomy, it is important to determine how much of this anatomy is heritable and how much develops as a response to environmental factors during life. We estimated heritability for vertebral counts as well as typical cervical, thoracic, and lumbar elements from 210 individuals from the pedigreed Cayo Santiago Macaca mulatta skeletal collection. We found moderate heritability of vertebral counts (h2 = 0.216-0.326), but with strong heritability of the type of variation (e.g., a tendency to meristic or homeotic change) in the vertebral count (h2 = 0.599), suggesting a possible explanation for high variability in vertebral numbers among the hominoids in particular. The moderate heritability of vertebral count also suggests that vertebral count is an unsuitable metric for estimating the ancestral state for some taxa. We found strong heritability in the morphology of cervical and upper lumbar zygapophyseal facets (h2 = 0.548-0.550) and the thoracic spinous processes (h2 = 0.609-0.761), including high heritability of the spinous process angle in the upper thoracic and upper lumbar elements (h2 = 0.649-0.752). We suggest these are related to maintaining stability in the cervical and lumbar regions, and reducing motion in the thoracic region, respectively. We propose that spinous processes may contain greater phylogenetic information, whereas transverse processes may contain greater information of function 'in life'. We also found important size effects, suggesting that size is the most heritable component of overall form and largely responsible for intertrait differences. This suggests that it is inappropriate to indiscriminately remove size effects from morphological comparisons.

RNA Metabolism and the Role of Small RNAs in Regulating Multiple Aspects of RNA Metabolism

RNA metabolism is focused on RNA molecules and encompasses all the crucial processes an RNA molecule may or will undergo throughout its life cycle. It is an essential cellular process that allows all cells to function effectively. The transcriptomic landscape of a cell is shaped by the processes such as RNA biosynthesis, maturation (RNA processing, folding, and modification), intra- and inter-cellular transport, transcriptional and post-transcriptional regulation, modification, catabolic decay, and retrograde signaling, all of which are interconnected and are essential for cellular RNA homeostasis. In eukaryotes, sRNAs, typically 20-31 nucleotides in length, are a class of ncRNAs found to function as nodes in various gene regulatory networks. sRNAs are known to play significant roles in regulating RNA population at the transcriptional, post-transcriptional, and translational levels. Along with sRNAs, such as miRNAs, siRNAs, and piRNAs, new categories of ncRNAs, i.e., lncRNAs and circRNAs, also contribute to RNA metabolism regulation in eukaryotes. In plants, various genetic screens have demonstrated that sRNA biogenesis mutants, as well as RNA metabolism pathway mutants, exhibit similar growth and development defects, misregulated primary and secondary metabolism, as well as impaired stress response. In addition, sRNAs are both the "products" and the "regulators" in broad RNA metabolism networks; gene regulatory networks involving sRNAs form autoregulatory loops that affect the expression of both sRNA and the respective target. This review examines the interconnected aspects of RNA metabolism with sRNA regulatory pathways in plants. It also explores the potential conservation of these pathways across different kingdoms, particularly in plants and animals. Additionally, the review highlights how cellular RNA homeostasis directly impacts adaptive responses to environmental changes as well as different developmental aspects in plants.

Genetic Association Between Polycystic Ovary Syndrome and the APOA5 rs662799 and PLIN1 rs894160 Metabolic Variants in the Western Saudi Population: A Case-Control Study

Background

Polycystic ovary syndrome (PCOS) is a common endocrinological condition affecting women of reproductive age, associated with insulin resistance and obesity. PCOS pathogenesis is complex and multifactorial, involving genetic and environmental factors.

Objectives

This study aimed to determine and compare genotype and allele frequencies of single nucleotide polymorphisms (SNPs) in the apolipoprotein A5 (APOA5; rs662799) and perilipin 1 (PLIN1; rs894160, rs1052700 and rs6496589) genes in Western Saudi women to investigate their association with PCOS and its clinical characteristics.

Design and methods

This was a case-control study conducted on women with (n = 104) and without (n = 87) PCOS. The SNPs were genotyped using TaqMan genotyping assays.

Results

Significant and direct associations were detected between PCOS susceptibility and APOA5 SNP rs662799 and PLIN1 SNP rs894160 (P < .001). For APOA5 SNP rs662799, women with the A allele were more likely to have PCOS (relative risk [RR] = 1.348, odds ratio [OR] = 2.313, P < .001) and hypertriglyceridaemia (OR = 17.0, P = .5) than women with the G allele. For PLIN1 SNP rs894160, women with the T allele were more likely to have PCOS than women with the C allele (RR = 8.043, OR = 7.427, P < .001). For PLIN1 SNP rs1052700, women with the TT genotype were more likely to have hyperandrogenism (OR = 29.75, P = .02) and an irregular period (OR = 0.07, P = .040) than women with the AT genotype.

Conclusion

We identified novel alleles and genotypes contributing to the genetic risk of PCOS in the Western Saudi population.

Targeting the key players of phenotypic plasticity in cancer cells by phytochemicals

Plasticity of phenotypic traits refers to an organism's ability to change in response to environmental stimuli. As a result, the response may alter an organism's physiological state, morphology, behavior, and phenotype. Phenotypic plasticity in cancer cells describes the considerable ability of cancer cells to transform phenotypes through non-genetic molecular signaling activities that promote therapy evasion and tumor metastasis via amplifying cancer heterogeneity. As a result of metastable phenotypic state transitions, cancer cells can tolerate chemotherapy or develop transient adaptive resistance. Therefore, new findings have paved the road in identifying factors and agents that inhibit or suppress phenotypic plasticity. It has also investigated novel multitargeted agents that may promise new effective strategies in cancer treatment. Despite the efficiency of conventional chemotherapeutic agents, drug toxicity, development of resistance, and high-cost limit their use in cancer therapy. Recent research has shown that small molecules derived from natural sources are capable of suppressing cancer by focusing on the plasticity of phenotypic responses. This systematic, comprehensive, and critical review analyzes the current state of knowledge regarding the ability of phytocompounds to target phenotypic plasticity at both preclinical and clinical levels. Current challenges/pitfalls, limitations, and future perspectives are also discussed.

Development as explanation: Understanding phenotypic stability and variability after the failure of genetic determinism

In the predominately gene-centered view of 20th century biology, the relationship between genotype and phenotype was essentially a relationship between cause and effect, between a plan and a product. Abandoning the idea of genes as inherited instructions or blueprints for phenotypes raises the question of how to best account for observed phenotypic stability and variability within and across generations of a population. We argue that the processes responsible for phenotypic stability and the processes responsible for phenotypic variability are one and the same, namely, the dynamics of development. This argument proposes that stability of phenotypic form is found not because of the transmission of genotypes, genetic programs, or the transfer of internal blueprints, but because similar internal and external conditions-collectively conceptualized as resources of development-can be reliably reconstituted in each generation. Variability of phenotypic form, which is an indispensable feature of any evolving system, relies on these same resources, but because the internal and external conditions of development are not reconstituted identically in succeeding generations, these conditions-and the phenotypes to which they give rise-will always be characterized by at least some variability.

Developmental Programming by Perinatal Glucocorticoids

Early-life environmental factors can have persistent effects on physiological functions by altering developmental procedures in various organisms. Recent experimental and epidemiological studies now further support the idea that developmental programming is also present in mammals, including humans, influencing long-term health. Although the mechanism of programming is still largely under investigation, the role of endocrine glucocorticoids in developmental programming is gaining interest. Studies found that perinatal glucocorticoids have a persistent effect on multiple functions of the body, including metabolic, behavioral, and immune functions, in adulthood. Several mechanisms have been proposed to play a role in long-term programming. In this review, recent findings on this topic are summarized and the potential biological rationale behind this phenomenon is discussed.

Complex delayed and transgenerational effects driven by the interaction of heat and insecticide in the maternal generation of the wheat aphid, Sitobion avenae

BACKGROUND

Experience of an earlier environment plays an important role in the induction of delayed and even intergenerational phenotypes of an organism. Evidence suggests that rapid adaptation to an environmental stressor can change the performance of organisms, and even enable them to deal with other stressors. The goal of this study was to determine the effects of adult imidacloprid exposure on life-history traits within and between generations of the cereal aphid, Sitobion avenae, under three developmental conditions: constant temperature, 22°C; a low-intensity thermal condition, 22 + 34°C for 2 h per day; and a high-intensity thermal condition, 22 + 38°C for 2 h per day.

RESULTS

Early thermal experience not only changed the tolerance of S. avenae to the insecticide, imidacloprid, but also caused adults to incur fitness costs: the higher the heat intensity, the higher the costs. Negative transgenerational impacts of combined heat and insecticide stressors were limited to the developmental stage, whereas positive stimulation of heat intensity was observed during the adult stage. Overall, nymphal thermal experience exacerbated the detrimental effects of adult insecticidal exposure on the intrinsic rate of population increase in the maternal generation, but stimulated a net reproductive rate in the succeeding offspring generation.

CONCLUSION

These findings underpin the importance of considering the experience of the early developmental environment, but also enhance our understanding of the transgenerational effects of combined thermal and insecticide stressors on the population fate of S. avenae. They also help to assess the efficacy of chemical control in a warming world. © 2021 Society of Chemical Industry.

Thyroid hormones regulate the formation and environmental plasticity of white bars in clownfishes

Determining how plasticity of developmental traits responds to environmental conditions is a challenge that must combine evolutionary sciences, ecology, and developmental biology. During metamorphosis, fish alter their morphology and color pattern according to environmental cues. We observed that juvenile clownfish (Amphiprion percula) modulate the developmental timing of their adult white bar formation during metamorphosis depending on the sea anemone species in which they are recruited. We observed an earlier formation of white bars when clownfish developed with Stichodactyla gigantea (Sg) than with Heteractis magnifica (Hm). As these bars, composed of iridophores, form during metamorphosis, we hypothesized that timing of their development may be thyroid hormone (TH) dependent. We treated clownfish larvae with TH and found that white bars developed earlier than in control fish. We further observed higher TH levels, associated with rapid white bar formation, in juveniles recruited in Sg than in Hm, explaining the faster white bar formation. Transcriptomic analysis of Sg recruits revealed higher expression of duox, a dual oxidase implicated in TH production as compared to Hm recruits. Finally, we showed that duox is an essential regulator of iridophore pattern timing in zebrafish. Taken together, our results suggest that TH controls the timing of adult color pattern formation and that shifts in duox expression and TH levels are associated with ecological differences resulting in divergent ontogenetic trajectories in color pattern development.

Socioeconomic position, immune function, and its physiological markers

The development of costly traits such as immune function and secondary sexual traits is constrained by resource availability. The quality of developmental conditions and the availability of resources in ontogeny may therefore influence immune system functions and other biological traits. We analyzed causal pathways between family socioeconomic position, strength of immune response, and five physiological biomarkers in young Latvian men (n = 93) using structural equation modeling. Men from wealthier families had higher testosterone levels (r_s = 0.280), stronger immune response (r_s = 0.551), and higher facial attractiveness (r_s = 0.300). There were weak, non-significant correlations between family income, body fat percentage (r_s = -0.147), and fluctuating asymmetry (r_s = -0.159). Testosterone partially (33.8%) mediated the effect of family income on facial masculinity. Testosterone (positively) and adiposity (negatively) partially (4%) mediated the relationship between family income and immune function. Higher facial masculinity, higher facial symmetry, and lower adiposity were reliable and independent cues of better immune function (R² = 0.238) in a larger sample of young Latvian men (N = 146). Resource availability in ontogeny has an important role for the development of immune function and physical appearance, and it is a key parameter to be included in human eco-immunological research.

Integrative developmental biology in the age of anthropogenic change

Humans are changing and challenging nature in many ways. Conservation Biology seeks to limit human impacts on nature and preserve biological diversity. Traditionally, Developmental Biology and Conservation Biology have had nonoverlapping objectives, operating in distinct spheres of biological science. However, this chasm can and should be filled to help combat the emerging challenges of the 21st century. The means by which to accomplish this goal were already established within the conceptual framework of evo- and eco-devo and can be further expanded to address the ways that anthropogenic disturbance affect embryonic development. Herein, I describe ways that these approaches can be used to advance the study of reptilian embryos. More specifically, I explore the ways that a developmental perspective can advance ongoing studies of embryonic physiology in the context of global warming and chemical pollution, both of which are known stressors of reptilian embryos. I emphasize ways that these developmental perspectives can inform conservation biologists trying to develop management practices that will address the complexity of challenges facing reptilian embryos.

Population Genomics of an Anadromous Hilsa Shad Tenualosa ilisha Species across Its Diverse Migratory Habitats: Discrimination by Fine-Scale Local Adaptation

The migration of anadromous fish in heterogenic environments unceasingly imposes a selective pressure that results in genetic variation for local adaptation. However, discrimination of anadromous fish populations by fine-scale local adaptation is challenging because of their high rate of gene flow, highly connected divergent population, and large population size. Recent advances in next-generation sequencing (NGS) have expanded the prospects of defining the weakly structured population of anadromous fish. Therefore, we used NGS-based restriction site-associated DNA (NextRAD) techniques on 300 individuals of an anadromous Hilsa shad (Tenualosa ilisha) species, collected from nine strategic habitats, across their diverse migratory habitats, which include sea, estuary, and different freshwater rivers. The NextRAD technique successfully identified 15,453 single nucleotide polymorphism (SNP) loci. Outlier tests using the FST OutFLANK and pcadapt approaches identified 74 and 449 SNPs (49 SNPs being common), respectively, as putative adaptive loci under a divergent selection process. Our results, based on the different cluster analyses of these putatively adaptive loci, suggested that local adaptation has divided the Hilsa shad population into two genetically structured clusters, in which marine and estuarine collection sites were dominated by individuals of one genetic cluster and different riverine collection sites were dominated by individuals of another genetic cluster. The phylogenetic analysis revealed that all the riverine populations of Hilsa shad were further subdivided into the north-western riverine (turbid freshwater) and the north-eastern riverine (clear freshwater) ecotypes. Among all of the putatively adaptive loci, only 36 loci were observed to be in the coding region, and the encoded genes might be associated with important biological functions related to the local adaptation of Hilsa shad. In summary, our study provides both neutral and adaptive contexts for the observed genetic divergence of Hilsa shad and, consequently, resolves the previous inconclusive findings on their population genetic structure across their diverse migratory habitats. Moreover, the study has clearly demonstrated that NextRAD sequencing is an innovative approach to explore how dispersal and local adaptation can shape genetic divergence of non-model anadromous fish that intersect diverse migratory habitats during their life-history stages.

Early life starvation has stronger intra-generational than transgenerational effects on key life-history traits and consumption measures in a sawfly

Resource availability during development shapes not only adult phenotype but also the phenotype of subsequent offspring. When resources are absent and periods of starvation occur in early life, such developmental stress often influences key life-history traits in a way that benefits individuals and their offspring when facing further bouts of starvation. Here we investigated the impacts of different starvation regimes during larval development on life-history traits and measures of consumption in the turnip sawfly, Athalia rosae (Hymenoptera: Tenthredinidae). We then assessed whether offspring of starved and non-starved parents differed in their own life-history if reared in conditions that either matched that of their parents or were a mismatch. Early life starvation effects were more pronounced within than across generations in A. rosae, with negative impacts on adult body mass and increases in developmental time, but no effects on adult longevity in either generation. We found some evidence of higher growth rates in larvae having experienced starvation, although this did not ameliorate the overall negative effect of larval starvation on adult size. However, further work is necessary to disentangle the effects of larval size and instar from those of starvation treatment. Finally, we found weak evidence for transgenerational effects on larval growth, with intra-generational larval starvation experience being more decisive for life-history traits. Our study demonstrates that intra-generational effects of starvation are stronger than transgenerational effects on life-history traits and consumption measures in A. rosae.

Chemically induced plasticity in early life history of Palaemon argentinus: are chemical alarm cues conserved within palaemonid shrimps?

Most aquatic animals use infochemicals from both conspecifics and heterospecifics to assess local predation risks and enhance predator detection. Released substances from injured conspecifics and other species (chemical alarm cues) are reliable cues to indicate an imminent danger in a specific habitat and often mediate the development of inducible defenses. Amphibian and fish embryos have been shown to acquire this information while at the embryonic stage of development, in relation to the developing nervous system and sensory development. With the exception of Daphnia, there is no information on chemically mediated responses to alarm cues in embryos of any crustacean groups. Therefore, we tested whether embryo exposure to chemical cues simulating predation on conspecifics or heterospecifics (closely related, non-coexisting species), or a mixture of both, alters embryonic developmental time, size and morphology of the first larval instar in Palaemon argentinus (Crustacea: Decapoda). Embryonic exposure to chemical alarm cues from conspecifics shortened the embryonic developmental time and elicited larger larvae with a longer rostrum. Rostrum length of the first larval instar changed independently of their size, thus elongated rostra can be considered a defensive feature. Embryonic developmental time was not altered by chemical alarm cues from either heterospecifics or the mixed cues treatment; however, exposure to these cues resulted in larger larvae compared with the control group. Chemically induced morphological plasticity in larvae in response to alarm cues from con- and heterospecifics suggests that such cues are conserved in palaemonids shrimps, providing embryos with an innate recognition of heterospecific alarm cues as predicted by the phylogenetic relatedness hypothesis.

Exploring the molecular aspects associated with testicular germ cell tumors: a review

Testicular germ cell tumors (TGCTs) represent the most common solid tumors affecting young men. They constitute a distinct entity because of their embryonic origin and their unique biological behavior. Recent preclinical data regarding biological signaling machinery as well as genetic and epigenetic mechanisms associated with molecular patterns of tumors have contribute to explain the pathogenesis and the differentiation of TGCTs and to understand the mechanisms responsible for the development of resistance to treatment. In this review, we discuss the main genetic and epigenetic events associated with TGCTs development in order to better define their role in the pathogenesis of these tumors and in cisplatin-acquired resistance.

Genomic responses to the socio-sexual environment in male Drosophila melanogaster exposed to conspecific rivals

Socio-sexual environments have profound effects on fitness. Local sex ratios can alter the threat of sexual competition, to which males respond via plasticity in reproductive behaviors and ejaculate composition. In Drosophila melanogaster, males detect the presence of conspecific, same-sex mating rivals prior to mating using multiple, redundant sensory cues. Males that respond to rivals gain significant fitness benefits by altering mating duration and ejaculate composition. Here we investigated the underlying genome-wide changes involved. We used RNA-seq to analyze male transcriptomic responses 2, 26, and 50 h after exposure to rivals, a time period that was previously identified as encompassing the major facets of male responses to rivals. The results showed a strong early activation of multiple sensory genes in the head-thorax (HT), prior to the expression of any phenotypic differences. This gene expression response was reduced by 26 h, at the time of maximum phenotypic change, and shut off by 50 h. In the abdomen (A), fewer genes changed in expression and gene expression responses appeared to increase over time. The results also suggested that different sets of functionally equivalent genes might be activated in different replicates. This could represent a mechanism by which robustness is conferred upon highly plastic traits. Overall, our study reveals that mRNA-seq can identify subtle genomic signatures characteristic of flexible behavioral phenotypes.

Incubation Temperature Alters Temperature-Dependent Oxygen Consumption in Northern Bobwhite Quail Hatchlings (Colinus virginianus)

This study investigated the effect of mismatching incubation and posthatch temperatures in northern bobwhite quail hatchlings. Quail embryos were incubated at 35.5° or 37.5°C. Metabolic rates were then measured in hatchlings acclimated to either the same or the opposite temperature treatment. While hatchlings expressed higher oxygen consumption when posthatch temperature did not match incubation temperature, the effect of mismatching temperatures was significant only when posthatch temperature was higher than incubation temperature. Our data suggest that bobwhite quail hatchlings may express increased metabolism due to mismatches between incubation and posthatch temperatures. More specifically, the nature or direction of the mismatch can determine the magnitude of the metabolic effect. These findings highlight the importance of considering the context of specific conditions experienced throughout ontogeny when observing phenotypic outcomes.

A loss of heterozygosity, a loss in competition? The effects of inbreeding, pre- and postnatal conditions on nestling development

The early developmental trajectory is affected by genetic and environmental factors that co‐depend and interact often in a complex way. In order to distinguish their respective roles, we used canaries (Serinus canaria) of different genetic backgrounds (inbred and outbred birds). An artificial size hierarchy was created to provoke within‐nest competition, manipulating postnatal conditions. To this end, inbred birds were weight‐matched with outbred birds into duos, and each nest contained one duo of size‐advantaged, and one duo of size‐disadvantaged inbred and outbred nestlings. Prenatal (maternal) effects were taken into account also, enabling us to study the separate as well as the interactive effects of inbreeding, pre‐ and postnatal conditions on nestling development. We find that postnatal conditions were the most important determinant of early growth, with size‐advantaged nestlings growing faster and obtaining larger size/body mass at fledging in comparison with size‐disadvantaged nestlings. Prenatal conditions were important too, with birds that hatched from eggs that were laid late in the laying order obtaining a larger size at fledging than those hatched from early laid eggs. Inbreeding inhibited growth, but surprisingly this did not depend on (dis)advantageous pre‐ or postnatal conditions. Our findings imply that inbred individuals lose when they are in direct competition with same‐sized outbred individuals regardless of the rearing conditions, and we thus propose that reduced competitiveness is one of the driving forces of inbreeding depression.

Short-term exposure to predation affects body elemental composition, climbing speed and survival ability in Drosophila melanogaster

Factors such as temperature, habitat, larval density, food availability and food quality substantially affect organismal development. In addition, risk of predation has a complex impact on the behavioural and morphological life history responses of prey. Responses to predation risk seem to be mediated by physiological stress, which is an adaptation for maintaining homeostasis and improving survivorship during life-threatening situations. We tested whether predator exposure during the larval phase of development has any influence on body elemental composition, energy reserves, body size, climbing speed and survival ability of adult Drosophila melanogaster. Fruit fly larvae were exposed to predation by jumping spiders (Phidippus apacheanus), and the percentage of carbon (C) and nitrogen (N) content, extracted lipids, escape response and survival were measured from predator-exposed and control adult flies. The results revealed predation as an important determinant of adult phenotype formation and survival ability. D. melanogaster reared together with spiders had a higher concentration of body N (but equal body C), a lower body mass and lipid reserves, a higher climbing speed and improved adult survival ability. The results suggest that the potential of predators to affect the development and the adult phenotype of D. melanogaster is high enough to use predators as a more natural stimulus in laboratory experiments when testing, for example, fruit fly memory and learning ability, or when comparing natural populations living under different predation pressures.

Why do we need theories?

Theories organize knowledge and construct objectivity by framing observations and experiments. The elaboration of theoretical principles is examined in the light of the rich interactions between physics and mathematics. These two disciplines share common principles of construction of concepts and of the proper objects of inquiry. Theory construction in physics relies on mathematical symmetries that preserve the key invariants observed and proposed by such theory; these invariants buttress the idea that the objects of physics are generic and thus interchangeable and they move along specific trajectories which are uniquely determined, in classical and relativistic physics. In contrast to physics, biology is a historical science that centers on the changes that organisms experience while undergoing ontogenesis and phylogenesis. Biological objects, namely organisms, are not generic but specific; they are individuals. The incessant changes they undergo represent the breaking of symmetries, and thus the opposite of symmetry conservation, a central component of physical theories. This instability corresponds to the changes of the environment and the phenotypes. Inspired by Galileo's principle of inertia, the "default state" of inert matter, we propose a "default state" for biological dynamics following Darwin's first principle, "descent with modification" that we transform into "proliferation with variation and motility" as a property that spans life, including cells in an organism. These dissimilarities between theories of the inert and of biology also apply to causality: biological causality is to be understood in relation to the distinctive role that constraints assume in this discipline. Consequently, the notion of cause will be reframed in a context where constraints to activity are seen as the core component of biological analyses. Finally, we assert that the radical materiality of life rules out distinctions such as "software vs. hardware."

Phenotypic Novelty in EvoDevo: The Distinction Between Continuous and Discontinuous Variation and Its Importance in Evolutionary Theory

The introduction of novel phenotypic structures is one of the most significant aspects of organismal evolution. Yet the concept of evolutionary novelty is used with drastically different connotations in various fields of research, and debate exists about whether novelties represent features that are distinct from standard forms of phenotypic variation. This article contrasts four separate uses for novelty in genetics, population genetics, morphology, and behavioral science, before establishing how novelties are used in evolutionary developmental biology (EvoDevo). In particular, it is detailed how an EvoDevo-specific research approach to novelty produces insight distinct from other fields, gives the concept explanatory power with predictive capacities, and brings new consequences to evolutionary theory. This includes the outlining of research strategies that draw attention to productive areas of inquiry, such as threshold dynamics in development. It is argued that an EvoDevo-based approach to novelty is inherently mechanistic, treats the phenotype as an agent with generative potential, and prompts a distinction between continuous and discontinuous variation in evolutionary theory.

The importance of trans-generational effects in Lepidoptera

The importance of trans-generational effects in shaping an individuals’ phenotype and fitness, and consequently even impacting population dynamics is increasingly apparent. Most of the research on trans-generational effects still focuses on plants, mammals, and birds. In the past few years, however, increasing number of studies, especially on maternal effects, have highlighted their importance also in many insect systems. Lepidoptera, specifically butterflies, have been used as model systems for studying the role of phenotypic plasticity within generations. As ectotherms, they are highly sensitive to environmental variation, and indeed many butterflies show adaptive phenotypic plasticity in response to environmental conditions. Here, we synthesize what is known about trans-generational effects in Lepidoptera, compile evidence for different environmental cues that are important drivers of trans-generational effects, and point out which offspring traits are mainly impacted. Finally, we emphasize directions for future research that are needed for better understanding of the adaptive nature of trans-generational effects in Lepidoptera in particular, but potentially also in other organisms.

Overcrowding-mediated stress alters cell proliferation in key neuroendocrine areas during larval development in Rhinella arenarum

Exposure to adverse environmental conditions can elicit a stress response, which results in an increase in endogenous corticosterone levels. In early life stages, it has been thoroughly demonstrated that amphibian larval growth and development is altered as a consequence of chronic stress by interfering with the metamorphic process, however, the underlying mechanisms involved have only been partially disentangled. We examined the effect of intraspecific competition on corticosterone levels during larval development of the toad Rhinella arenarum and its ultimate effects on cell proliferation in particular brain areas as well as the pituitary gland. While overcrowding altered the number of proliferating cells in the pituitary gland, hypothalamus, and third ventricle of the brain, no differences were observed in areas which are less associated with neuroendocrine processes, such as the first ventricle of the brain. Apoptosis was increased in hypothalamic regions but not in the pituitary. With regards to pituitary cell populations, thyrotrophs but not somatoatrophs and corticotrophs showed a decrease in the cell number in overcrowded larvae. Our study shows that alterations in growth and development, produced by stress, results from an imbalance in the neuroendocrine systems implicated in orchestrating the timing of metamorphosis.

Anthropogenic host plant expansion leads a nettle-feeding butterfly out of the forest: consequences for larval survival and developmental plasticity in adult morphology

Recent anthropogenic eutrophication has meant that host plants of nettle-feeding insects became quasi-omnipresent in fertile regions of Western Europe. However, host plant resource quality – in terms of microclimate and nutritional value – may vary considerably between the ‘original’ forest habitat and ‘recent’ agricultural habitat. Here, we compared development in both environmental settings using a split-brood design, so as to explore to what extent larval survival and adult morphology in the nettle-feeding butterfly Aglais urticae are influenced by the anthropogenic environment. Nettles along field margins had higher C/N ratios and provided warmer microclimates to larvae. Larvae developed 20% faster and tended to improve their survival rates, on the agricultural land compared to woodland. Our split-brood approach indicated plastic responses within families, but also family effects in the phenotypic responses. Adult males and females had darker wing pigmentation in the drier and warmer agricultural environment, which contrasts with the thermal melanism hypothesis. Developmental plasticity in response to this microclimatically different and more variable habitat was associated with a broader phenotypic parameter space for the species. Both habitat expansion and developmental plasticity are likely contributors to the ecological and evolutionary success of these nettle-feeding insects in anthropogenic environments under high nitrogen load.

Estrogens in the wrong place at the wrong time: Fetal BPA exposure and mammary cancer

Iatrogenic gestational exposure to diethylstilbestrol (DES) induced alterations of the genital tract and predisposed individuals to develop clear cell carcinoma of the vagina as well as breast cancer later in life. Gestational exposure of rodents to a related compound, the xenoestrogen bisphenol-A (BPA) increases the propensity to develop mammary cancer during adulthood, long after cessation of exposure. Exposure to BPA during gestation induces morphological alterations in both the stroma and the epithelium of the fetal mammary gland at 18 days of age. We postulate that the primary target of BPA is the fetal stroma, the only mammary tissue expressing estrogen receptors during fetal life. BPA would then alter the reciprocal stroma-epithelial interactions that mediate mammogenesis. In addition to this direct effect on the mammary gland, BPA is postulated to affect the hypothalamus and thus in turn affect the regulation of mammotropic hormones at puberty and beyond.

Early environment influences later performance in fishes

Conditions fish encounter during embryogenesis and early life history can leave lasting effects not only on morphology, but also on growth rate, life-history and behavioural traits. The ecology of offspring can be affected by conditions experienced by their parents and mother in particular. This review summarizes such early impacts and their ecological influences for a variety of teleost species, but with special reference to salmonids. Growth and adult body size, sex ratio, egg size, lifespan and tendency to migrate can all be affected by early influences. Mechanisms behind such phenotypically plastic impacts are not well known, but epigenetic change appears to be one central mechanism. The thermal regime during development and incubation is particularly important, but also early food consumption and intraspecific density can all be responsible for later life-history variation. For behavioural traits, early experiences with effects on brain, sensory development and cognition appear essential. This may also influence boldness and other social behaviours such as mate choice. At the end of the review, several issues and questions for future studies are given.

Regulatory gene networks that shape the development of adaptive phenotypic plasticity in a cichlid fish

Phenotypic plasticity is the ability of organisms with a given genotype to develop different phenotypes according to environmental stimuli, resulting in individuals that are better adapted to local conditions. In spite of their ecological importance, the developmental regulatory networks underlying plastic phenotypes often remain uncharacterized. We examined the regulatory basis of diet-induced plasticity in the lower pharyngeal jaw (LPJ) of the cichlid fish Astatoreochromis alluaudi, a model species in the study of adaptive plasticity. Through raising juvenile A. alluaudi on either a hard or soft diet (hard-shelled or pulverized snails) for between 1 and 8 months, we gained insight into the temporal regulation of 19 previously identified candidate genes during the early stages of plasticity development. Plasticity in LPJ morphology was first detected between 3 and 5 months of diet treatment. The candidate genes, belonging to various functional categories, displayed dynamic expression patterns that consistently preceded the onset of morphological divergence and putatively contribute to the initiation of the plastic phenotypes. Within functional categories, we observed striking co-expression, and transcription factor binding site analysis was used to examine the prospective basis of their coregulation. We propose a regulatory network of LPJ plasticity in cichlids, presenting evidence for regulatory crosstalk between bone and muscle tissues, which putatively facilitates the development of this highly integrated trait. Through incorporating a developmental time-course into a phenotypic plasticity study, we have identified an interconnected, environmentally responsive regulatory network that shapes the development of plasticity in a key innovation of East African cichlids.

[Cancer and the elusive cancer genes]

For almost a century, the somatic mutation theory (SMT) has been the prevalent theory to explain carcinogenesis. The SMT posits that the accumulation of mutations in the genome of a single normal cell is responsible for the transformation of such cell into a neoplasm. Implicitly, this theory claims that the default state of cells in metazoan is quiescence and that cancer is a cell-based, genetic and molecular disease. From lessons learned while performing our own research on control of cell proliferation and while adopting an organicist perspective, in 1999, we proposed a competing theory, the tissue organization field theory (TOFT). In contraposition to the SMT, (1) the TOFT posits that cancer is a tissue-based disease whereby carcinogens (directly) and mutations in the germ-line (indirectly) may alter normal interactions between the stroma and their adjacent epithelium. And (2) the TOFT explicitly acknowledges that the default state of all cells is proliferation and motility, a premise that is relevant to and compatible with evolutionary theory. Theoretical arguments and experimental evidence are presented to compare the merits of the original SMT and its variants and those of the TOFT in organizing principles, construct objectivity, and ultimately explain carcinogenesis.

In absence of local adaptation, plasticity and spatially varying selection rule: a view from genomic reaction norms in a panmictic species (Anguilla rostrata)

Background

American eel (Anguilla rostrata) is one of the few species for which panmixia has been demonstrated at the scale of the entire species. As such, the development of long term local adaptation is impossible. However, both plasticity and spatially varying selection have been invoked in explaining how American eel may cope with an unusual broad scope of environmental conditions. Here, we address this question through transcriptomic analyses and genomic reaction norms of eels from two geographic origins reared in controlled environments.

Results

The null hypothesis of no difference in gene expression between eels from the two origins was rejected. Many unique transcripts and two out of seven gene clusters showed significant difference in expression, both at time of capture and after three months of common rearing. Differences in expression were observed at numerous genes representing many functional groups when comparing eels from a same origin reared under different salinity conditions. Plastic response to different rearing conditions varied among gene clusters with three clusters showing significant origin-environment interactions translating into differential genomic norms of reaction. Most genes and functional categories showing differences between origins were previously shown to be differentially expressed in a study comparing transcription profiles between adult European eels acclimated to different salinities.

Conclusions

These results emphasize that while plasticity in expression may be important, there is also a role for local genetic (and/or epigenetic) differences in explaining differences in gene expression between eels from different geographic origins. Such differences match those reported in genetically distinct populations in other fishes, both in terms of the proportion of genes that are differentially expressed and the diversity of biological functions involved. We thus propose that genetic differences between glass eels of different origins caused by spatially varying selection due to local environmental conditions translates into transcriptomic differences (including different genomic norms of reaction) which may in turn explain part of the phenotypic variance observed between different habitats colonized by eels.

Effects of resource variation during early life and adult social environment on contest outcomes in burying beetles: a context-dependent silver spoon strategy?

Good early nutritional conditions may confer a lasting fitness advantage over individuals suffering poor early conditions (a ‘silver spoon’ effect). Alternatively, if early conditions predict the likely adult environment, adaptive plastic responses might maximize individual performance when developmental and adult conditions match (environmental-matching effect). Here, we test for silver spoon and environmental-matching effects by manipulating the early nutritional environment of Nicrophorus vespilloides burying beetles. We manipulated nutrition during two specific early developmental windows: the larval environment and the post-eclosion environment. We then tested contest success in relation to variation in adult social environmental quality experienced (defined according to whether contest opponents were smaller (good environment) or larger (poor environment) than the focal individual). Variation in the larval environment influenced adult body size but not contest success per se for a given adult social environment experienced (an ‘indirect’ silver spoon effect). Variation in post-eclosion environment affected contest success dependent on the quality of the adult environment experienced (a context-dependent ‘direct’ silver spoon effect). By contrast, there was no evidence for environmental-matching. The results demonstrate the importance of social environmental context in determining how variation in nutrition in early life affects success as an adult.

The origins of variation: evolutionary insights from developmental science

Evidence from contemporary epigenetic research indicates that it is not biologically meaningful to discuss genes without reference to the molecular, cellular, organismal, and environmental context within which they are activated and expressed. Genetic and nongenetic factors, including those beyond the organism, constitute a dynamic relational developmental system. This insight highlights the importance of bringing together genetics, development, and ecology into one explanatory framework for a more complete understanding of the emergence and maintenance of phenotypic stability and variability. In this Chapter, I review some examples of this integrative effort and explore its implications for developmental and evolutionary science, with a particular emphasis on the origins of phenotypic novelty. I argue that developmental science is critical to this integrative effort, in that evolutionary explanation cannot be complete without developmental explanation. This is the case because the process of development generates the phenotypic variation on which natural selection can act.

Bisphenol A and phthalates and endometriosis: the Endometriosis: Natural History, Diagnosis and Outcomes Study

OBJECTIVE

To explore the relation between bisphenol A and 14 phthalate metabolites and endometriosis.

DESIGN

Matched cohort design.

SETTING

Fourteen clinical centers.

PATIENT(S)

The operative cohort comprised 495 women undergoing laparoscopy/laparotomy, whereas the population cohort comprised 131 women matched on age and residence.

INTERVENTION(S)

None.

MAIN OUTCOME MEASURE(S)

Surgically visualized or pelvic magnetic resonance imaging diagnosed endometriosis in the two cohorts, respectively.

RESULT(S)

Odds ratios (OR) and 95% confidence intervals (CIs) were estimated using logistic regression adjusting for age, body mass index, and creatinine. In the population cohort, six phthalate metabolites-mono-n-butyl phthalate, mono-[(2-carboxymethyl) hexyl] phthalate, mono (2-ethyl-5-carboxyphentyl) phthalate, mono (2-ethylhexyl) phthalate, mono (2-ethyl-5-hydroxyhexyl) phthalate, and mono (2-ethyl-5-oxohexyl) phthalate-were significantly associated with an approximately twofold increase in the odds of an endometriosis diagnosis. Two phthalates were associated with endometriosis in the operative cohort when restricting to visualized and histologic endometriosis (monooctyl phthalate; OR 1.38; 95% CI 1.10-1.72) or when restricting comparison women to those with a postoperative diagnosis of a normal pelvis [mono (2-ethylhexyl) phthalate; OR 1.35; 95% CI 1.03-1.78].

CONCLUSION(S)

Select phthalates were associated with higher odds of an endometriosis diagnosis for women with magnetic resonance imaging-diagnosed endometriosis. The lack of consistency of findings across cohorts underscores the impact of methodology on findings.

Early developmental gene regulation in Strongylocentrotus purpuratus embryos in response to elevated CO₂ seawater conditions

Ocean acidification, or the increased uptake of CO(2) by the ocean due to elevated atmospheric CO(2) concentrations, may variably impact marine early life history stages, as they may be especially susceptible to changes in ocean chemistry. Investigating the regulatory mechanisms of early development in an environmental context, or ecological development, will contribute to increased understanding of potential organismal responses to such rapid, large-scale environmental changes. We examined transcript-level responses to elevated seawater CO(2) during gastrulation and the initiation of spiculogenesis, two crucial developmental processes in the purple sea urchin, Strongylocentrotus purpuratus. Embryos were reared at the current, accepted oceanic CO(2) concentration of 380 microatmospheres (μatm), and at the elevated levels of 1000 and 1350 μatm, simulating predictions for oceans and upwelling regions, respectively. The seven genes of interest comprised a subset of pathways in the primary mesenchyme cell gene regulatory network (PMC GRN) shown to be necessary for the regulation and execution of gastrulation and spiculogenesis. Of the seven genes, qPCR analysis indicated that elevated CO(2) concentrations only had a significant but subtle effect on two genes, one important for early embryo patterning, Wnt8, and the other an integral component in spiculogenesis and biomineralization, SM30b. Protein levels of another spicule matrix component, SM50, demonstrated significant variable responses to elevated CO(2). These data link the regulation of crucial early developmental processes with the environment that these embryos would be developing within, situating the study of organismal responses to ocean acidification in a developmental context.

Environmentally induced epigenetic transgenerational inheritance of phenotype and disease

Environmental epigenetics has an important role in regulating phenotype formation or disease etiology. The ability of environmental factors and exposures early in life to alter somatic cell epigenomes and subsequent development is a critical factor in how environment affects biology. Environmental epigenetics provides a molecular mechanism to explain long term effects of environment on the development of altered phenotypes and "emergent" properties, which the "genetic determinism" paradigm cannot. When environmental factors permanently alter the germ line epigenome, then epigenetic transgenerational inheritance of these environmentally altered phenotypes and diseases can occur. This environmental epigenetic transgenerational inheritance of phenotype and disease is reviewed with a systems biology perspective.

Pre- and post-natal stress in context: effects on the stress physiology in a precocial bird

Developmental stress can significantly influence physiology and survival in many species. Mammalian studies suggest that pre- and post-natal stress can cause different effects (i.e. hyper- or hypo-responsiveness) on the Hypothalamic-Pituitary-Adrenal axis (HPA axis), the main mediator of the stress response. In mammals, the physiological intimacy between mother and offspring constrains the possibility to control, and therefore to manipulate, maternal pre- and post-natal influences. Here, by using the Japanese quail (Coturnix c. japonica) as our model, we elevated the glucocorticoid stress hormone corticosterone in ovo and/or in the endogenous circulation of hatchlings. We examined the effects of treatments on corticosterone and glucose stress responses at two different ages, in juvenile and adult quail. In juveniles, corticosterone data revealed a sex-specific effect of post-natal treatment regardless of the previous pre-natal protocol, with post-natally treated females showing shorter stress responses in comparison with the other groups, while no differences were observed among males. In adulthood, birds previously stressed as embryos showed higher corticosterone concentrations over the stress response compared with controls. This effect was not evident in birds subjected to either post- or the combined treatments. There were no effects on glucose in the juveniles. However, adult birds previously stressed in ovo showed opposite sex-specific basal glucose patterns compared with the other groups. Our results demonstrate that (1) early glucocorticoid exposure can have both transient and long-term effects on the HPA axis, depending upon the developmental stage and sex and (2) post-natal stress can modulate the effects of pre-natal stress on HPA activity.

Developmental exposure to endocrine-disrupting chemicals programs for reproductive tract alterations and obesity later in life

Many chemicals in the environment, especially those with estrogenic activity, are able to disrupt the programming of endocrine signaling pathways established during development; these chemicals are referred to as endocrine-disrupting chemicals. Altered programming can result in numerous adverse consequences in estrogen-target tissues, some of which may not be apparent until later in life. For example, a wide variety of structural, functional, and cellular effects have been identified in reproductive tract tissues. In addition to well-documented reproductive changes, obesity and diabetes have joined the list of adverse effects that have been associated with developmental exposure to environmental estrogens and other endocrine-disrupting chemicals. Obesity is a significant public health problem reaching epidemic proportions worldwide. Experimental animal studies document an association of developmental exposure to environmental estrogens and obesity. For example, a murine model of perinatal exposure to diethylstilbestrol has proven useful in studying mechanisms involved in abnormal programming of differentiating estrogen-target tissues, including reproductive tract tissues and adipocytes. Other environmental estrogens, including the environmental contaminant bisphenol A, have also been linked to reproductive problems and obesity later in life. Epidemiology studies support similar findings in humans, as do studies of cells in culture. Together, these findings suggest new targets for abnormal programming by estrogenic chemicals and provide evidence supporting the scientific concept termed the developmental origins of adult disease. Furthermore, the association of environmental estrogens with obesity and diabetes expands the focus on these diseases from intervention or treatment to include prevention or avoidance of chemical modifiers, especially during critical windows of development.

Antennal cropping during colony foundation in termites

The literature on pairing and mating behavior in termites indicates that a number of distal antennal segments in dealates of both sexes are often removed during colony foundation, with terms such as amputation, mutilation and cannibalism typically employed to report the phenomenon. Here we propose the use of the phrase 'antennal cropping' to describe the behavior, and assess naturally occurring levels of its occurrence by comparing the number of antennal segments in museum specimens of alates and dealates in 16 species of Australian termites (four families), supplemented by analyzing published data on Coptotermes gestroi. Dealates had significantly fewer antennal segments than alates in 14 of the 16 termite species, with both exceptions belonging to the family Termitidae. Levels of antennal cropping were not significantly different between the sexes but did vary by family. Dealates in the Kalotermitidae removed the most segments (41.3%) and those in the Termitidae removed the fewest (8.9%). We discuss the biological significance of this phylogenetically widespread termite behavior, and suggest that controlled antennal cropping is not only a normal part of their behavioral repertoire but also a key influence that changes the conduct and physiology of the royal pair during the initial stages of colony foundation.

The use of the zebrafish model in stress research

The study of the causes and mechanisms underlying psychiatric disorders requires the use of non-human models for the test of scientific hypotheses as well as for use in pre-clinical drug screening and discovery. This review argues in favor of the use of zebrafish as a novel animal model to study the impact of early (stressful) experiences on the development of differential stress phenotypes in later life. This phenomenon is evolutionary conserved among several vertebrate species and has relevance to the etiology of psychiatric disorders. Why do we need novel animal models? Although significant progress has been achieved with the use of traditional mammalian models, there are major pitfalls associated with their use that impedes progress on two major fronts: 1) uncovering of the molecular mechanisms underlying aspects of compromised (stress-exposed) brain development relevant to the etiology of psychiatric disorders, and 2) ability to develop high-throughput technology for drug discovery in the field of psychiatry. The zebrafish model helps resolve these issues. Here we present a conceptual framework for the use of zebrafish in stress research and psychiatry by addressing three specific domains of application: 1) stress research, 2) human disease mechanisms, and 3) drug discovery. We also present novel methodologies associated with the development of the zebrafish stress model and discuss how such methodologies can contribute to remove the main bottleneck in the field of drug discovery.

Physics and the canalization of morphogenesis: a grand challenge in organismal biology

Morphogenesis takes place against a background of organism-to-organism and environmental variation. Therefore, fundamental questions in the study of morphogenesis include: How are the mechanical processes of tissue movement and deformation affected by that variability, and in turn, how do the mechanic of the system modulate phenotypic variation? We highlight a few key factors, including environmental temperature, embryo size and environmental chemistry that might perturb the mechanics of morphogenesis in natural populations. Then we discuss several ways in which mechanics-including feedback from mechanical cues-might influence intra-specific variation in morphogenesis. To understand morphogenesis it will be necessary to consider whole-organism, environment and evolutionary scales because these larger scales present the challenges that developmental mechanisms have evolved to cope with. Studying the variation organisms express and the variation organisms experience will aid in deciphering the causes of birth defects.

Cancer as development gone awry: the case for bisphenol-A as a carcinogen

The discovery of a rare clear cell carcinoma of the vagina in young women gestationally exposed to the estrogen diethylstilbestrol (DES) lent empirical support to the hypothesis that prenatal exposure to xenoestrogens might cause cancer. This fact contradicted two well-accepted notions: (i) mammalian development was merely the unfolding of a genetic program and (ii) only mutagenic agents could cause cancer. The ecological developmental biology (eco–devo) movement revitalized the concept of developmental plasticity through the occurrence of polyphenisms whereby a single genotype produces diverse phenotypes which are determined by environmental cues. Based on the principles of eco–devo and the tissue organization field theory of carcinogenesis, we hypothesized that developmental exposure to xenoestrogens increased the propensity to develop mammary cancer during adulthood. Bisphenol-A (BPA), a ubiquitous xenoestrogen, was chosen as a model for environmental estrogen exposure. In mice, perinatal exposure to environmentally relevant BPA levels induced alterations of the mammary gland architecture which manifested during fetal morphogenesis and throughout life, including the development of pre-neoplastic lesions. In rats, gestational exposure to BPA induced pre-neoplastic lesions and carcinoma in situ that manifested in adulthood in the absence of any additional treatment. Emerging epidemiological data reveal an increased incidence of breast cancer in women exposed to DES during gestation. Hence, both animal experiments and epidemiological data strengthen the hypothesis that fetal exposure to xenoestrogens may be an underlying cause of the increased incidence of breast cancer observed over the past 50 years.