Developmental plasticity and the evolution of animal complex life cycles

Within- and transgenerational stress legacy effects of ocean acidification on red abalone (Haliotis rufescens) growth and survival

Understanding the mechanisms by which individual organisms respond and populations adapt to global climate change is a critical challenge. The role of plasticity and acclimation, within and across generations, may be essential given the pace of change. We investigated plasticity across generations and life stages in response to ocean acidification (OA), which poses a growing threat to both wild populations and the sustainable aquaculture of shellfish. Most studies of OA on shellfish focus on acute effects, and less is known regarding the longer term carryover effects that may manifest within or across generations. We assessed these longer term effects in red abalone (Haliotis rufescens) using a multi-generational split-brood experiment. We spawned adults raised in ambient conditions to create offspring that we then exposed to high pCO2 (1180 μatm; simulating OA) or low pCO2 (450 μatm; control or ambient conditions) during the first 3 months of life. We then allowed these animals to reach maturity in ambient common garden conditions for 4 years before returning the adults into high or low pCO2 treatments for 11 months and measuring growth and reproductive potential. Early-life exposure to OA in the F1 generation decreased adult growth rate even after 5 years especially when abalone were re-exposed to OA as adults. Adult but not early-life exposure to OA negatively impacted fecundity. We then exposed the F2 offspring to high or low pCO2 treatments for the first 3 months of life in a fully factorial, split-brood design. We found negative transgenerational effects of parental OA exposure on survival and growth of F2 offspring, in addition to significant direct effects of OA on F2 survival. These results show that the negative impacts of OA can last within and across generations, but that buffering against OA conditions at critical life-history windows can mitigate these effects.

Spatially and Temporally Distributed Complexity-A Refreshed Framework for the Study of GRN Evolution

Irrespective of the heuristic value of interpretations of developmental processes in terms of gene regulatory networks (GRNs), larger-angle views often suffer from: (i) an inadequate understanding of the relationship between genotype and phenotype; (ii) a predominantly zoocentric vision; and (iii) overconfidence in a putatively hierarchical organization of animal body plans. Here, we constructively criticize these assumptions. First, developmental biology is pervaded by adultocentrism, but development is not necessarily egg to adult. Second, during development, many unicells undergo transcriptomic profile transitions that are comparable to those recorded in pluricellular organisms; thus, their study should not be neglected from the GRN perspective. Third, the putatively hierarchical nature of the animal body is mirrored in the GRN logic, but in relating genotype to phenotype, independent assessments of the dynamics of the regulatory machinery and the animal’s architecture are required, better served by a combinatorial than by a hierarchical approach. The trade-offs between spatial and temporal aspects of regulation, as well as their evolutionary consequences, are also discussed. Multicellularity may derive from a unicell’s sequential phenotypes turned into different but coexisting, spatially arranged cell types. In turn, polyphenism may have been a crucial mechanism involved in the origin of complex life cycles.

Molecular and morphological characterisation of Diplostomum phoxini (Faust, 1918) with a revised classification and an updated nomenclature of the species-level lineages of Diplostomum (Digenea: Diplostomidae) sequenced worldwide

We characterised morphologically and molecularly Diplostomum phoxini (Faust, 1918) based on cercarial isolates from the snail Ampullaceana balthica (L.) (Gastropoda: Lymnaeidae) and metacercariae from the Eurasian minnow, Phoxinus phoxinus (L.) (Cypriniformes: Leuciscidae), and provided molecular evidence for the identification of the snail intermediate host. Phylogenetic analyses based on the cytochrome c oxidase subunit 1 (cox1) gene depicted 44 molecularly characterised species and genetically distinct lineages of Diplostomum, and resulted in: (i) a re-identification/re-classification of 98 isolates plus D. baeri sampled in North America; (ii) re-definition of the composition of the D. baeri species complex which now includes nine molecularly characterised species/lineages; (iii) re-definition of the composition of the D. mergi species complex which now includes seven molecularly characterised species/lineages; and (iv) an updated nomenclature for the molecularly characterised species-level lineages of Diplostomum.

Molecular signatures of the rediae, cercariae and adult stages in the complex life cycles of parasitic flatworms (Digenea: Psilostomatidae)

Background

Parasitic flatworms (Trematoda: Digenea) represent one of the most remarkable examples of drastic morphological diversity among the stages within a life cycle. Which genes are responsible for extreme differences in anatomy, physiology, behavior, and ecology among the stages? Here we report a comparative transcriptomic analysis of parthenogenetic and amphimictic generations in two evolutionary informative species of Digenea belonging to the family Psilostomatidae.

Methods

In this study the transcriptomes of rediae, cercariae and adult worm stages of Psilotrema simillimum and Sphaeridiotrema pseudoglobulus, were sequenced and analyzed. High-quality transcriptomes were generated, and the reference sets of protein-coding genes were used for differential expression analysis in order to identify stage-specific genes. Comparative analysis of gene sets, their expression dynamics and Gene Ontology enrichment analysis were performed for three life stages within each species and between the two species.

Results

Reference transcriptomes for P. simillimum and S. pseudoglobulus include 21,433 and 46,424 sequences, respectively. Among 14,051 orthologous groups (OGs), 1354 are common and specific for two analyzed psilostomatid species, whereas 13 and 43 OGs were unique for P. simillimum and S. pseudoglobulus, respectively. In contrast to P. simillimum, where more than 60% of analyzed genes were active in the redia, cercaria and adult worm stages, in S. pseudoglobulus less than 40% of genes had such a ubiquitous expression pattern. In general, 7805 (36.41%) and 30,622 (65.96%) of genes were preferentially expressed in one of the analyzed stages of P. simillimum and S. pseudoglobulus, respectively. In both species 12 clusters of co-expressed genes were identified, and more than a half of the genes belonging to the reference sets were included into these clusters. Functional specialization of the life cycle stages was clearly supported by Gene Ontology enrichment analysis.

Conclusions

During the life cycles of the two species studied, most of the genes change their expression levels considerably, consequently the molecular signature of a stage is not only a unique set of expressed genes, but also the specific levels of their expression. Our results indicate unexpectedly high level of plasticity in gene regulation between closely related species. Transcriptomes of P. simillimum and S. pseudoglobulus provide high quality reference resource for future evolutionary studies and comparative analyses.

A case of nascent speciation: unique polymorphism of gonophores within hydrozoan Sarsia lovenii

Revealing the mechanisms of life cycle changes is critical for understanding the processes driving hydrozoan evolution. Our analysis of mitochondrial (COI, 16S) and nuclear (ITS1 and ITS2) gene fragments resulted in the discovery of unique polymorphism in the life cycle of Sarsia lovenii from the White Sea. This polymorphic species exhibits two types of gonophores: hydroids produce both free-swimming medusae and attached medusoids (phenotypic polymorphism). Our phylogenetic analysis revealed the intrinsic genetic structure of S. lovenii (genetic polymorphism). Two haplogroups inhabiting the White Sea differ in their reproductive modes. Haplogroup 1 produces attached medusoids, and haplogroup 2 produces free-swimming medusae. Our experiments indicated the possibility of free interbreeding between haplogroups that likely is a rare event in the sea. We propose that inter-haplogroup crossing of S. lovenii in the White Sea may be limited by discordance in periods of spawning or by spatial differences in habitat of spawning specimens. Our finding can be interpreted as a case of nascent speciation that illustrates the patterns of repeated medusa loss in hydrozoan evolution. Life cycle traits of S. lovenii may be useful for elucidating the molecular mechanisms of medusa reduction in hydrozoans.

Emergence of diverse life cycles and life histories at the origin of multicellularity

The evolution of multicellularity has given rise to a remarkable diversity of multicellular life cycles and life histories. Whereas some multicellular organisms are long-lived, grow through cell division, and repeatedly release single-celled propagules (for example, animals), others are short-lived, form by aggregation, and propagate only once, by generating large numbers of solitary cells (for example, cellular slime moulds). There are no systematic studies that explore how diverse multicellular life cycles can come about. Here, we focus on the origin of multicellularity and develop a mechanistic model to examine the primitive life cycles that emerge from a unicellular ancestor when an ancestral gene is co-opted for cell adhesion. Diverse life cycles readily emerge, depending on ecological conditions, group-forming mechanism, and ancestral constraints. Among these life cycles, we recapitulate both extremes of long-lived groups that propagate continuously and short-lived groups that propagate only once, with the latter type of life cycle being particularly favoured when groups can form by aggregation. Our results show how diverse life cycles and life histories can easily emerge at the origin of multicellularity, shaped by ancestral constraints and ecological conditions. Beyond multicellularity, this finding has similar implications for other major transitions, such as the evolution of sociality.

Plasticity of thermal tolerance and its relationship with growth rate in juvenile mussels (Mytilus californianus)

Complex life cycles characterized by uncertainty at transitions between larval/juvenile and adult environments could favour irreversible physiological plasticity at such transitions. To assess whether thermal tolerance of intertidal mussels (Mytilus californianus) adjusts to post-settlement environmental conditions, we collected juveniles from their thermally buffered microhabitat from high- and low-shore locations at cool (wave-exposed) and warm (wave-protected) sites. Juveniles were transplanted to unsheltered cages at the two low sites or placed in a common garden. Juveniles transplanted to the warm site for one month in summer had higher thermal tolerance, regardless of origin site. By contrast, common-garden juveniles from all sites had lower tolerance indistinguishable from exposed site transplants. After six months in the field plus a common garden period, there was a trend for higher thermal tolerance at the protected site, while reduced thermal tolerance at both sites indicated seasonal acclimatization. Thermal tolerance and growth rate were inversely related after one but not six months; protected-site transplants were more tolerant but grew more slowly. In contrast to juveniles, adults from low-shore exposed and protected sites retained differences in thermal tolerance after common garden treatment in summer. Both irreversible and reversible forms of plasticity must be considered in organismal responses to changing environments.

Introduction to Genome Biology and Diversity

Organisms display astonishing levels of cell and molecular diversity, including genome size, shape, and architecture. In this chapter, we review how the genome can be viewed as both a structural and an informational unit of biological diversity and explicitly define our intended meaning of genetic information. A brief overview of the characteristic features of bacterial, archaeal, and eukaryotic cell types and viruses sets the stage for a review of the differences in organization, size, and packaging strategies of their genomes. We include a detailed review of genetic elements found outside the primary chromosomal structures, as these provide insights into how genomes are sometimes viewed as incomplete informational entities. Lastly, we reassess the definition of the genome in light of recent advancements in our understanding of the diversity of genomic structures and the mechanisms by which genetic information is expressed within the cell. Collectively, these topics comprise a good introduction to genome biology for the newcomer to the field and provide a valuable reference for those developing new statistical or computation methods in genomics. This review also prepares the reader for anticipated transformations in thinking as the field of genome biology progresses.

Phenotypic Plasticity in Animals Exposed to Osmotic Stress - Is it Always Adaptive?

Hyperplasia and hypertrophy are elements of phenotypic plasticity adjusting organ size and function. Because they are costly, we assume that they are beneficial. In this review, the authors discuss examples of tissue and organ systems that respond with plastic changes to osmotic stress to raise awareness that we do not always have sufficient experimental evidence to conclude that such processes provide fitness advantages. Changes in hydranth architecture in the hydroid Cordylophora caspia or variations in size in the anal papillae of insect larvae upon changes in medium salinity may be adaptive or not. The restructuring of salt glands in ducklings upon salt-loading is an example of phenotypic plasticity which indeed seems beneficial. As the genomes of model species are recently sequenced and the animals are easy to rear, these species are suitable study objects to investigate the biological significance of phenotypic plasticity and to study potential epigenetic and other mechanisms underlying phenotypic changes.

De novo Assembly of the Burying Beetle Nicrophorus orbicollis (Coleoptera: Silphidae) Transcriptome Across Developmental Stages with Identification of Key Immune Transcripts

Burying beetles (Nicrophorus spp.) are among the relatively few insects that provide parental care while not belonging to the eusocial insects such as ants or bees. This behavior incurs energy costs as evidenced by immune deficits and shorter life-spans in reproducing beetles. In the absence of an assembled transcriptome, relatively little is known concerning the molecular biology of these beetles. This work details the assembly and analysis of the Nicrophorus orbicollis transcriptome at multiple developmental stages. RNA-Seq reads were obtained by next-generation sequencing and the transcriptome was assembled using the Trinity assembler. Validation of the assembly was performed by functional characterization using Gene Ontology (GO), Eukaryotic Orthologous Groups (KOG), and Kyoto Encyclopedia of Genes and Genomes (KEGG) analyses. Differential expression analysis highlights developmental stage-specific expression patterns, and immunity-related transcripts are discussed. The data presented provides a valuable molecular resource to aid further investigation into immunocompetence throughout this organism's sexual development.

Predicting phenological shifts in a changing climate

Phenological shifts constitute one of the clearest manifestations of climate warming. Advanced emergence is widely reported in high-latitude ectotherms, but a significant number of species exhibit delayed, or no change in, emergence. Here we present a mechanistic theoretical framework that reconciles these disparate observations and predicts population-level phenological patterns based solely on data on temperature responses of the underlying life history traits. Our model, parameterized with data from insects at different latitudes, shows that peak abundance occurs earlier in the year when warming increases the mean environmental temperature, but is delayed when warming increases the amplitude of seasonal fluctuations. We find that warming does not necessarily lead to a longer activity period in high-latitude species because it elevates summer temperatures above the upper limit for reproduction and development. Our findings both confirm and confound expectations for ectotherm species affected by climate warming: an increase in the mean temperature is more detrimental to low-latitude species adapted to high mean temperatures and low-amplitude seasonal fluctuations; an increase in seasonal fluctuations is more detrimental to high-latitude species adapted to low mean temperatures and high-amplitude fluctuations.

Rhipicephalus sanguineus (Acari: Ixodidae) species complex: morphometric and ultrastructural analyses

Although some studies have already been performed on Rhipicephalus sanguineus (Latreille) populations, there is still much disarray around its taxonomic classification. Rhipicephalus sanguineus, which is also known as " (brown dog tick) is a three-host tick that parasitizes many vertebrates, including occasional human hosts. It presents a worldwide distribution and is a vector of zoonosis with acknowledged public health importance. In Western Europe, R. turanicus (Pomerantsev) share many phenotypic features and is genetically closely related to R. sanguineus. Additionally, as these species are sympatric, they can be easily misidentified. However, by means of a thorough morphological traits analysis, it is possible to distinguish both species, especially resorting to scanning electron microscopy. This study was conducted using stereoscopic and SEM analyses, both associated with morphometric analysis, in order to help clarify the taxonomic status of this species complex. For that purpose, specimens resembling R. sanguineus were collected from dogs of the Midwestern Iberian Peninsula. Identification was performed based on taxonomical key characteristics. The obtained results allowed the authors to agree that a great morphological variability is found within R. sanguineus-like Iberian populations. Nevertheless, R. turanicus is easily identified by morphologic analysis, especially using reference specimens, and its presence in Portugal is suggested.

Molecular, biological, and morphometric comparisons between different geographical populations of Rhipicephalus sanguineus sensu lato (Acari: Ixodidae)

In this study, different geographical populations of Rhipicephalus sanguineus sensu lato were compared by molecular, biological, and morphometric methods. Phylogenetic trees were constructed using 12S and 16S rDNA sequences and showed two distinct clades: one composed of ticks from Brazil (Jaboticabal, SP), Cuba (Havana) Thailand (Bangkok) and the so-called "tropical strain" ticks. The second clade was composed of ticks from Spain (Zaragoza), Argentina (Rafaela, Santa Fe) and the so-called "temperate strain" ticks. Morphometric analysis showed good separation between females of the two clades and within the temperate clade. Males also exhibited separation between the two clades, but with some overlap. Multiple biological parameters revealed differences between the two clades, especially the weight of the engorged female. These results confirm the existence of at least two species under the name "R. sanguineus".

Eco-evolutionary feedback and the tuning of proto-developmental life cycles

Multicellular organisms depend on developmental programs to coordinate growth and differentiation from single cells, but the origins of development are unclear. A possible starting point is stochastic phenotypic variation generated by molecular noise. Given appropriate environmental conditions, noise-driven differentiation could conceivably evolve so as to come under regulatory control; however, abiotic conditions are likely to be restrictive. Drawing from an experimental system, we present a model in which environmental fluctuations are coupled to population growth. We show that this coupling generates stable selection for a single optimal strategy that is largely insensitive to environmental conditions, including the number of competitors, carrying capacity of the environment, difference in growth rates among phenotypic variants, and population density. We argue that this optimal strategy establishes stabilizing conditions likely to improve the quality and reliability of information experienced by evolving organisms, thus increasing opportunity for the evolutionary emergence of developmental programs.

A conceptual model for the origin of worker behaviour and adaptation of eusociality

In a model based on the wasp family Vespidae, the origin of worker behaviour, which constitutes the eusociality threshold, is not based on relatedness, therefore the origin of eusociality does not depend on inclusive fitness, and workers at the eusociality threshold are not altruistic. Instead, incipient workers and queens behave selfishly and are subject to direct natural selection. Beyond the eusociality threshold, relatedness enables 'soft inheritance' as the framework for initial adaptations of eusociality. At the threshold of irreversibility, queen and worker castes become fixed in advanced eusociality. Transitions from solitary to facultative, facultative to primitive, and primitive to advanced eusociality occur via exaptation, phenotypic accommodation and genetic assimilation. Multilevel selection characterizes the solitary to highly eusocial transition, but components of multilevel selection vary across levels of eusociality. Roles of behavioural flexibility and developmental plasticity in the evolutionary process equal or exceed those of genotype.

Evolution and molecular mechanisms of adaptive developmental plasticity

Aside from its selective role in filtering inter-individual variation during evolution by natural selection, the environment also plays an instructive role in producing variation during development. External environmental cues can influence developmental rates and/or trajectories and lead to the production of distinct phenotypes from the same genotype. This can result in a better match between adult phenotype and selective environment and thus represents a potential solution to problems posed by environmental fluctuation. The phenomenon is called adaptive developmental plasticity. The study of developmental plasticity integrates different disciplines (notably ecology and developmental biology) and analyses at all levels of biological organization, from the molecular regulation of changes in organismal development to variation in phenotypes and fitness in natural populations. Here, we focus on recent advances and examples from morphological traits in animals to provide a broad overview covering (i) the evolution of developmental plasticity, as well as its relevance to adaptive evolution, (ii) the ecological significance of alternative environmentally induced phenotypes, and the way the external environment can affect development to produce them, (iii) the molecular mechanisms underlying developmental plasticity, with emphasis on the contribution of genetic, physiological and epigenetic factors, and (iv) current challenges and trends, including the relevance of the environmental sensitivity of development to studies in ecological developmental biology, biomedicine and conservation biology.

Evolutionary lability of a complex life cycle in the aphid genus Brachycaudus

Background

Most aphid species complete their life cycle on the same set of host-plant species, but some (heteroecious species) alternate between different hosts, migrating from primary (woody) to secondary (herbaceous) host plants. The evolutionary processes behind the evolution of this complex life cycle have often been debated. One widely accepted scenario is that heteroecy evolved from monoecy on woody host plants. Several shifts towards monoecy on herbaceous plants have subsequently occurred and resulted in the radiation of aphids. Host alternation would have persisted in some cases due to developmental constraints preventing aphids from shifting their entire life cycle to herbaceous hosts (which are thought to be more favourable). According to this scenario, if aphids lose their primary host during evolution they should not regain it. The genus Brachycaudus includes species with all the types of life cycle (monoecy on woody plants, heteroecy, monoecy on herbs). We used this genus to test hypotheses concerning the evolution of life cycles in aphids.

Results

Phylogenetic investigation and character reconstruction suggest that life cycle is evolutionary labile in the genus. Though ancestral character states can be ambiguous depending on optimization methods, all analyses suggest that transitions from monoecy on herbs towards heteroecy have occurred several times. Transitions from heteroecy towards monoecy, are also likely. There have been many shifts in feeding behaviour but we found no significant correlation between life cycle changes and changes in diet.

Conclusions

The transitions from monoecy on herbs towards heteroecy observed in this study go against a widely accepted evolutionary scenario: aphids in the genus Brachycaudus seem to be able to recapture their supposedly ancestral woody host. This suggests that the determinants of host alternation are probably not as complicated as previously thought. Definitive proofs of the lability of life cycle in Brachycaudus will necessitate investigation of these determinants. Life cycle changes, whether corresponding to the loss or acquisition of a primary host, necessarily promote speciation, by inducing shifts of the reproductive phase on different plants. We suggest that the evolutionary lability of life cycle may have driven speciation events in the Brachycaudus genus.

Cheats as first propagules: a new hypothesis for the evolution of individuality during the transition from single cells to multicellularity

The emergence of individuality during the evolutionary transition from single cells to multicellularity poses a range of problems. A key issue is how variation in lower-level individuals generates a corporate (collective) entity with Darwinian characteristics. Of central importance to this process is the evolution of a means of collective reproduction, however, the evolution of a means of collective reproduction is not a trivial issue, requiring careful consideration of mechanistic details. Calling upon observations from experiments, we draw attention to proto-life cycles that emerge via unconventional routes and that transition, in single steps, individuality to higher levels. One such life cycle arises from conflicts among levels of selection and invokes cheats as a primitive germ line: it lays the foundation for collective reproduction, the basis of a self-policing system, the selective environment for the emergence of development, and hints at a plausible origin for a soma/germ line distinction.

Phenotypic plasticity in development and evolution: facts and concepts. Introduction

This theme issue pursues an exploration of the potential of taking into account the environmental sensitivity of development to explaining the evolution of metazoan life cycles, with special focus on complex life cycles and the role of developmental plasticity. The evolution of switches between alternative phenotypes as a response to different environmental cues and the evolution of the control of the temporal expression of alternative phenotypes within an organism's life cycle are here treated together as different dimensions of the complex relationships between genotype and phenotype, fostering the emergence of a more general and comprehensive picture of phenotypic evolution through a quite diverse sample of case studies. This introductory article reviews fundamental facts and concepts about phenotypic plasticity, adopting the most authoritative terminology in use in the current literature. The main topics are types and components of phenotypic variation, the evolution of organismal traits through plasticity, the origin and evolution of phenotypic plasticity and its adaptive value.