An integrative approach identifies developmental sequence heterochronies in freshwater basommatophoran snails

Comparative phenomics: a new approach to study heterochrony

Understanding the links between development and evolution is one of the major challenges of biology. 'Heterochronies', evolutionary alterations in the timings of development are posited as a key mechanism of evolutionary change, but their quantification requires gross simplification of organismal development. Consequently, how changes in event timings influence development more broadly is poorly understood. Here, we measure organismal development as spectra of energy in pixel values of video, creating high-dimensional landscapes integrating development of all visible form and function. This approach we termed 'Energy proxy traits' (EPTs) is applied alongside previously identified heterochronies in three freshwater pulmonate molluscs (Lymnaea stagnalis, Radix balthica and Physella acuta). EPTs were calculated from time-lapse video of embryonic development to construct a continuous functional time series. High-dimensional transitions in phenotype aligned with major sequence heterochronies between species. Furthermore, differences in event timings between conspecifics were associated with changes in high-dimensional phenotypic space. We reveal EPTs as a powerful approach to considering the evolutionary importance of alterations to developmental event timings. Reimagining the phenotype as energy spectra enabled continuous quantification of developmental changes in high-dimensional phenotypic space, rather than measurement of timings of discrete events. This approach has the possibility to transform how we study heterochrony and development more generally.

HeartCV: a tool for transferrable, automated measurement of heart rate and heart rate variability in transparent animals

Heart function is a key component of whole-organismal physiology. Bioimaging is commonly, but not exclusively, used for quantifying heart function in transparent individuals, including early developmental stages of aquatic animals, many of which are transparent. However, a central limitation of many imaging-related methods is the lack of transferability between species, life-history stages and experimental approaches. Furthermore, locating the heart in mobile individuals remains challenging. Here, we present HeartCV: an open-source Python package for automated measurement of heart rate and heart rate variability that integrates automated localization and is transferrable across a wide range of species. We demonstrate the efficacy of HeartCV by comparing its outputs with measurements made manually for a number of very different species with contrasting heart morphologies. Lastly, we demonstrate the applicability of the software to different experimental approaches and to different dataset types, such as those corresponding to longitudinal studies.

Spectral phenotyping of embryonic development reveals integrative thermodynamic responses

Background

Energy proxy traits (EPTs) are a novel approach to high dimensional organismal phenotyping that quantify the spectrum of energy levels within different temporal frequencies associated with mean pixel value fluctuations from video. They offer significant potential in addressing the phenotyping bottleneck in biology and are effective at identifying lethal endpoints and measuring specific functional traits, but the extent to which they might contribute additional understanding of the phenotype remains unknown. Consequently, here we test the biological significance of EPTs and their responses relative to fundamental thermodynamic principles. We achieve this using the entire embryonic development of Radix balthica, a freshwater pond snail, at different temperatures (20, 25 & 30 °C) and comparing responses against predictions from Arrhenius’ equation (Q₁₀ = 2).

Results

We find that EPTs are thermally sensitive and their spectra of frequency response enable effective high-dimensional treatment clustering throughout organismal development. Temperature-specific deviation in EPTs from thermodynamic predictions were evident and indicative of physiological mitigation, although they differed markedly in their responses from manual measures. The EPT spectrum was effective in capturing aspects of the phenotype predictive of biological outcomes, and suggest that EPTs themselves may reflect levels of energy turnover.

Conclusions

Whole-organismal biology is incredibly complex, and this contributes to the challenge of developing universal phenotyping approaches. Here, we demonstrate the biological relevance of a new holistic approach to phenotyping that is not constrained by preconceived notions of biological importance. Furthermore, we find that EPTs are an effective approach to measuring even the most dynamic life history stages.

Supplementary information

The online version contains supplementary material available at 10.1186/s12859-021-04152-1.

Frequent nonrandom shifts in the temporal sequence of developmental landmark events during teleost evolutionary diversification

Morphological transformations can be generated by evolutionary changes in the sequence of developmental events. In this study, we examined the evolutionary dynamics of the developmental sequence on a macroevolutionary scale in teleosts. Using the information from previous reports describing the development of 31 species, we extracted the developmental sequences of 19 landmark events involving the formation of phylogenetically conserved body parts; we then inferred ancestral developmental sequences by two different parsimony-based methods-event-pairing and continuous analysis. The phylogenetic comparisons of these sequences revealed event-dependent heterogeneity in the frequency of sequence changes. Most of the sequence changes occurred as exchanges of temporally neighboring events. These heterochronic changes in developmental sequences accumulated along evolutionary time, but the precise distribution of the changes over the teleostean phylogeny remains unclear due to technical limitations.

Heterokairy: a significant form of developmental plasticity?

There is a current surge of research interest in the potential role of developmental plasticity in adaptation and evolution. Here we make a case that some of this research effort should explore the adaptive significance of heterokairy, a specific type of plasticity that describes environmentally driven, altered timing of development within a species. This emphasis seems warranted given the pervasive occurrence of heterochrony, altered developmental timing between species, in evolution. We briefly review studies investigating heterochrony within an adaptive context across animal taxa, including examples that explore links between heterokairy and heterochrony. We then outline how sequence heterokairy could be included within the research agenda for developmental plasticity. We suggest that the study of heterokairy may be particularly pertinent in (i) determining the importance of non-adaptive plasticity, and (ii) embedding concepts from comparative embryology such as developmental modularity and disassociation within a developmental plasticity framework.

Developmental toxicity of metaldehyde in the embryos of Lymnaea stagnalis (Gastropoda: Pulmonata) co-exposed to the synergist piperonyl butoxide

Metaldehyde is a widely used molluscicide in countries where damage to crops from slugs and snails is a major problem associated with warm and wet winters. In the UK it is estimated that over 8% of the area covered by arable crops is treated with formulated granular bait pellets containing metaldehyde as the main active ingredient. Metaldehyde is hydrophilic (log Kow=0.12), water soluble (200 mg·L(-1) at 17 °C) and has been detected in UK surface waters in the concentration range of typically 0.2-0.6 μg·L(-1) (maximum 2.7 μg·L(-1)) during 2008-2011. In the absence of chronic data on potential hazards to non-target freshwater molluscs, a laboratory study was conducted to investigate the impact of metaldehyde on embryo development in the gastropod Lymnaea stagnalis (RENILYS strain) and using zinc as a positive control. L. stagnalis embryos were exposed to metaldehyde under semi-static conditions at 20±1 °C and hatching success and growth (measured as shell height and intraocular distance) examined after 21 d. Exposure concentrations were verified using HPLC and gave 21 d (hatching)NOEC and (hatching)LOEC mean measured values of 36 and 116 mg MET·L(-1), respectively (equal to the 21 d (shell height)NOEC and (shell height)LOEC values). For basic research purposes, a second group of L. stagnalis embryos was co-exposed to metaldehyde and the pesticide synergist piperonyl butoxide (PBO). Co-exposure to the PBO (measured concentrations between 0.47-0.56 mg·L(-1)) reduced hatching success from 100% to 47% and resulted in a 30% reduction in embryo growth (shell height) in snail embryos co-exposed to metaldehyde at 34-36 mg·L(-1) over 21 d. In conclusion, these data suggest mollusc embryos may have some metabolic detoxication capacity for metaldehyde and further work is warranted to explore this aspect in order to support the recent initiative to include molluscs in the OECD test guideline programme.

An embryonic transcriptome of the pulmonate snail Radix balthica

The pond snail, Radix balthica (Linnaeus 1758), is an emerging model species within ecological developmental biology. While its development has been characterised in detail, genomic resources for embryonic stages are lacking. We applied Illumina MiSeq RNA-seq to RNA isolated from pools of embryos at two points during development. Embryos were cultured in either the presence or absence of predator kariomones to increase the diversity of the transcripts assembled. Sequencing produced 47.2M paired-end reads, assembled into 54,360 contigs of which 73% were successfully annotated. This transcriptome provides an invaluable resource to build a mechanistic understanding of developmental plasticity.

Evolution of eumalacostracan development-new insights into loss and reacquisition of larval stages revealed by heterochrony analysis

BACKGROUND

Within Malacostraca (Crustacea), direct development and development through diverse forms of larvae are found. Recent investigations suggest that larva-related developmental features have undergone heterochronic evolution in Malacostraca. In the light of current phylogenetic hypotheses, the free-swimming nauplius larva was lost in the lineage leading to Malacostraca and evolved convergently in the malacostracan groups Dendrobranchiata and Euphausiacea. Here we reconstruct the evolutionary history of eumalacostracan (Malacostraca without Phyllocarida) development with regard to early appendage morphogenesis, muscle and central nervous system development, and determine the heterochronic transformations involved in changes of ontogenetic mode.

RESULTS

Timing of 33 developmental events from the different tissues was analyzed for six eumalacostracan species (material for Euphausiacea was not available) and one outgroup, using a modified version of Parsimov-based genetic inference (PGi). Our results confirm previous suggestions that the event sequence of nauplius larva development is partly retained in embryogenesis of those species which do not develop such a larva. The ontogenetic mode involving a nauplius larva was likely replaced by direct development in the malacostracan stem lineage. Secondary evolution of the nauplius larva of Dendrobranchiata from this ancestral condition, involved only a very small number of heterochronies, despite the drastic change of life history. In the lineage leading to Peracarida, timing patterns of nauplius-related development were lost. Throughout eumalacostracan evolution, events related to epidermal and neural tissue development were clearly less affected by heterochrony than events related to muscle development.

CONCLUSIONS

Weak integration between mesodermal and ectodermal development may have allowed timing in muscle formation to be altered independently of ectodermal development. We conclude that heterochrony in muscle development played a crucial role in evolutionary loss and secondary evolution of a nauplius larva in Malacostraca.

Challenges and opportunities in developmental integrative physiology

This review explores challenges and opportunities in developmental physiology outlined by a symposium at the 2014 American Physiological Society Intersociety Meeting: Comparative Approaches to Grand Challenges in Physiology. Across animal taxa, adverse embryonic/fetal environmental conditions can alter morphological and physiological phenotypes in juveniles or adults, and capacities for developmental plasticity are common phenomena. Human neonates with body sizes at the extremes of perinatal growth are at an increased risk of adult disease, particularly hypertension and cardiovascular disease. There are many rewarding areas of current and future research in comparative developmental physiology. We present key mechanisms, models, and experimental designs that can be used across taxa to investigate patterns in, and implications of, the development of animal phenotypes. Intraspecific variation in the timing of developmental events can be increased through developmental plasticity (heterokairy), and could provide the raw material for selection to produce heterochrony--an evolutionary change in the timing of developmental events. Epigenetics and critical windows research recognizes that in ovo or fetal development represent a vulnerable period in the life history of an animal, when the developing organism may be unable to actively mitigate environmental perturbations. 'Critical windows' are periods of susceptibility or vulnerability to environmental or maternal challenges, periods when recovery from challenge is possible, and periods when the phenotype or epigenome has been altered. Developmental plasticity may allow survival in an altered environment, but it also has possible long-term consequences for the animal. "Catch-up growth" in humans after the critical perinatal window has closed elicits adult obesity and exacerbates a programmed hypertensive phenotype (one of many examples of "fetal programing"). Grand challenges for developmental physiology include integrating variation in developmental timing within and across generations, applying multiple stressor dosages and stressor exposure at different developmental timepoints, assessment of epigenetic and parental influences, developing new animal models and techniques, and assessing and implementing these designs and models in human health and development.

Patterns of postcranial ossification and sequence heterochrony in bats: life histories and developmental trade-offs

The recently increased interest in studies on sequence heterochrony has uncovered developmental variation between species. However, how changes in developmental program are related to shifts in life-history parameters remains largely unsolved. Here we provide the most comprehensive data to date on postcranial ossification sequence of bats and compare them to various boreoeutherian mammals with different locomotive modes. Given that bats are equipped with an elongated manus, we expected to detect characteristic heterochronies particularly related to wing development. Although heterochronies related to wing development were confirmed as predicted, unexpected heterochronies regarding the pedal digits were also found. The timing of ossification onset of pedal phalanges is earlier than other mammals. Particularly, bats deviate from others in that pedal phalanges initiate ossification earlier than manual phalanges. It is known that the foot size of new born bats is close to that of adults, and that it takes several weeks to month until the wing is developed for flight. Given that the foot is required to be firm and stable enough at the time of birth to allow continued attachment to the mother and/or cave walls, we suggest that the accelerated development of the hind foot is linked to their unique life history. Since the forelimb is not mature enough for flight at birth and requires extended postnatal time to be large enough to be fully functional, we postulate that bats invest in earlier development of the hindlimb. We conclud that energy allocation trade-offs can play a significant role in shaping the evolution of development.

Analyzing developmental sequences with Parsimov--a case study of cranial muscle development in anuran larvae

Parsimov is a parsimony-based method for identifying the minimum number of heterochronic event-shifts on all branches of a given phylogenetic framework to explain the developmental sequences seen in the species investigated, and has been used to investigate the evolution of developmental sequences in various animal groups. However, the biological interpretation of the results is difficult not least because Parsimov uses non-independent data resulting from event-pairing as the basis for its analyses. To test the applicability of Parsimov to a large data set, larval cranial muscle development was studied in 15 anurans, three caudates and the Australian lungfish. We analyzed the developmental sequences with Parsimov to investigate: if there are (1) heterochronies on deep branches of a cladogram indicating changes in the ancestral sequences, (2) heterochronies that can be related to larval life-history, and (3) the sensitivity of the analysis to different underlying cladograms. We discovered general patterns of cranial muscle development, such as an anterior-to-posterior gradient, an outside-in pattern and a tendency for cranial muscles to develop from their region of origin toward their insertion. We found most heterochronies on terminal branches and only a few shifts on deep branches in the cladograms indicating changes in the ancestral sequences. No changes could be related to larval life-history. The underlying cladogram clearly influenced the outcome of the analysis. We propose that Parsimov has the potential, combined with other methods, to find evolutionary important changes and to aid the biological interpretation of these changes.

Parent--offspring similarity in the timing of developmental events: an origin of heterochrony?

Understanding the link between ontogeny (development) and phylogeny (evolution) remains a key aim of biology. Heterochrony, the altered timing of developmental events between ancestors and descendants, could be such a link although the processes responsible for producing heterochrony, widely viewed as an interspecific phenomenon, are still unclear. However, intraspecific variation in developmental event timing, if heritable, could provide the raw material from which heterochronies originate. To date, however, heritable developmental event timing has not been demonstrated, although recent work did suggest a genetic basis for intraspecific differences in event timing in the embryonic development of the pond snail, Radix balthica. Consequently, here we used high-resolution (temporal and spatial) imaging of the entire embryonic development of R. balthica to perform a parent-offspring comparison of the timing of twelve, physiological and morphological developmental events. Between-parent differences in the timing of all events were good predictors of such timing differences between their offspring, and heritability was demonstrated for two of these events (foot attachment and crawling). Such heritable intraspecific variation in developmental event timing could be the raw material for speciation events, providing a fundamental link between ontogeny and phylogeny, via heterochrony.

A genetic basis for intraspecific differences in developmental timing?

Heterochrony, altered developmental timing between ancestors and their descendents, has been proposed as a pervasive evolutionary feature and recent analytical approaches have confirmed its existence as an evolutionary pattern. Yet, the mechanistic basis for heterochrony remains unclear and, in particular, whether intraspecific variation in the timing of developmental events generates, or has the potential to generate, future between-species differences. Here we make a key step in linking heterochrony at the inter- and intraspecific level by reporting an association between interindividual variation in both the absolute and relative timing (position within the sequence of developmental events) of key embryonic developmental events and genetic distance for the pond snail, Radix balthica. We report significant differences in the genetic distance of individuals exhibiting different levels of dissimilarity in their absolute and relative timing of developmental events such as spinning activity, eyespot formation, heart ontogeny, and hatching. This relationship between genetic and developmental dissimilarity is consistent with there being a genetic basis for variation in developmental timing and so suggests that intraspecific heterochrony could provide the raw material for natural selection to produce speciation.

Predator cues alter the timing of developmental events in gastropod embryos

Heterochrony, differences in the timing of developmental events between descendent species and their ancestors, is a pervasive evolutionary pattern. However, the origins of such timing changes are still not resolved. Here we show, using sequence analysis, that exposure to predator cues altered the timing of onset of several developmental events in embryos of two closely related gastropod species: Radix balthica and Radix auricularia. These timing alterations were limited to certain events and were species-specific. Compared with controls, over half (62%) of exposed R. auricularia embryos had a later onset of body flexing and an earlier occurrence of the eyes and the heart; in R. balthica, 67 per cent of exposed embryos showed a later occurrence of mantle muscle flexing and an earlier attachment to, and crawling on, the egg capsule wall. The resultant developmental sequences in treated embryos converged, and were more similar to one another than were the sequences of the controls for both species. We conclude that biotic agents can elicit altered event timing in developing gastropod embryos. These changes were species-specific, but did not occur in all individuals. Such developmental plasticity in the timing of developmental events could be an important step in generating interspecific heterochrony.

Evolution of ossification sequences in salamanders and urodele origins assessed through event-pairing and new methods

Ossification sequences of the skull in extant Urodela and in Permo-Carboniferous Branchiosauridae have already been used to study the origin of lissamphibians. But most of these studies did not consider some recent methods developed to analyze the developmental sequences within a phylogenetic framework. Here, we analyze the ossification sequences of 24 cranial bones of 23 extant species of salamanders using the event-pairing method. This reveals new developmental synapomorphies for several extant salamander taxa and ancestral sequences for Urodela under four alternative reference phylogenies. An analysis with the 12 bones for which ossification sequence data are available in urodeles and in the branchiosaurid Apateon is also performed in order to compare the ancestral condition of the crown-group of Urodela to the sequence of Apateon. This reveals far more incompatibilities than previously suggested. The similarities observed between some extant salamanders and branchiosaurids may result from extensive homoplasy, as the extreme variation observed in extant Urodela suggests, or be plesiomorphic, as the conservation of some ossification patterns observed in other remotely related vertebrates like actinopterygians suggests. We propose a new, simpler method based on squared-change optimization to estimate the relative timing of ossification of various bones of hypothetical ancestors, and use independent-contrasts analysis to estimate the confidence intervals around these times. Our results show that the uncertainty of the ancestral ossification sequence of Urodela is much greater than event-pairing suggests. The developmental data do not allow to conclude that branchiosaurids are closely related to salamanders and their limited taxonomic distribution in Paleozoic taxa precludes testing hypotheses about lissamphibian origins. This is true regardless of the analytical method used (event-pairing or our new method based on squared-change parsimony). Simulations show that the new analytical method is generally more powerful to detect evolutionary shifts in developmental timing, and has lower Type I error rate than event-pairing. It also makes fewer errors in ancestral character value or state assignment than event-pairing.

Embryonic rotational behaviour in the pond snail Lymnaea stagnalis: influences of environmental oxygen and development stage

Responses of freshwater organisms to environmental oxygen tensions (PO(2)) have focused on adult (i.e. late developmental) stages, yet responses of embryonic stages to changes in environmental PO(2) must also have implications for organismal biology. Here we assess how the rotational behaviour of the freshwater snail Lymnaea stagnalis changes during development in response to conditions of hypoxia and hyperoxia. As rotation rate is linked to gas mixing in the fluid surrounding the embryo, we predicted that it would increase under hypoxic conditions but decrease under hyperoxia. Contrary to predictions, early, veliger stage embryos showed no change in their rotation rate under hyperoxia, and later, hippo stage embryos showed only a marginally significant increase in rotation under these conditions. Predictions for hypoxia were broadly supported, however, with both veliger and hippo stages showing a marked hypoxia-related increase in their rotation rates. There were also subtle differences between developmental stages, with hippos responding at PO(2)s (50% air saturation) greater than those required to elicit a similar response in veligers (20% air saturation). Differences between developmental stages also occurred on return to normoxic conditions following hypoxia: rotation in veligers returned to pre-exposure levels, whereas there was a virtual cessation in embryos at the hippo stage, likely the result of overstimulation of oxygen sensors driving ciliary movement in later, more developed embryos. Together, these findings suggest that the spinning activity of L. stagnalis embryos varies depending on environmental PO(2)s and developmental stage, increasing during hypoxia to mix capsular contents and maintain a diffusive gradient for oxygen entry into the capsule from the external environment ("stir-bar" theory of embryonic rotational behaviour).

A standard system to study vertebrate embryos

Staged embryonic series are important as reference for different kinds of biological studies. I summarise problems that occur when using ‘staging tables’ of ‘model organisms’. Investigations of developmental processes in a broad scope of taxa are becoming commonplace. Beginning in the 1990s, methods were developed to quantify and analyse developmental events in a phylogenetic framework. The algorithms associated with these methods are still under development, mainly due to difficulties of using non-independent characters. Nevertheless, the principle of comparing clearly defined newly occurring morphological features in development (events) in quantifying analyses was a key innovation for comparative embryonic research. Up to date no standard was set for how to define such events in a comparative approach. As a case study I compared the external development of 23 land vertebrate species with a focus on turtles, mainly based on reference staging tables. I excluded all the characters that are only identical for a particular species or general features that were only analysed in a few species. Based on these comparisons I defined 104 developmental characters that are common either for all vertebrates (61 characters), gnathostomes (26), tetrapods (3), amniotes (7), or only for sauropsids (7). Characters concern the neural tube, somite, ear, eye, limb, maxillary and mandibular process, pharyngeal arch, eyelid or carapace development. I present an illustrated guide listing all the defined events. This guide can be used for describing developmental series of any vertebrate species or for documenting specimen variability of a particular species. The guide incorporates drawings and photographs as well as consideration of species identifying developmental features such as colouration. The simple character-code of the guide is extendable to further characters pertaining to external and internal morphological, physiological, genetic or molecular development, and also for other vertebrate groups not examined here, such as Chondrichthyes or Actinopterygii. An online database to type in developmental events for different stages and species could be a basis for further studies in comparative embryology. By documenting developmental events with the standard code, sequence heterochrony studies (i.e. Parsimov) and studies on variability can use this broad comparative data set.

Cell lineage of the Ilyanassa embryo: evolutionary acceleration of regional differentiation during early development

Cell lineage studies in mollusk embryos have documented numerous variations on the lophotrochozoan theme of spiral cleavage. In the experimentally tractable embryo of the mud snail Ilyanassa, cell lineage has previously been described only up to the 29-cell stage. Here I provide a chronology of cell divisions in Ilyanassa to the stage of 84 cells (about 16 hours after first cleavage at 23°C), and show spatial arrangements of identified nuclei at stages ranging from 27 to 84 cells. During this period the spiral cleavage pattern gives way to a bilaterally symmetric, dorsoventrally polarized pattern of mitotic timing and geometry. At the same time, the mesentoblast cell 4d rapidly proliferates to form twelve cells lying deep to the dorsal ectoderm. The onset of epiboly coincides with a period of mitotic quiescence throughout the ectoderm. As in other gastropod embryos, cell cycle lengths vary widely and predictably according to cell identity, and many of the longest cell cycles occur in small daughters of highly asymmetric divisions. While Ilyanassa shares many features of embryonic cell lineage with two other caenogastropod genera, Crepidula and Bithynia, it is distinguished by a general tendency toward earlier and more pronounced diversification of cell division pattern along axes of later differential growth.

Timing of organogenesis support basal position of turtles in the amniote tree of life

Background

The phylogenetic position of turtles is the most disputed aspect in the reconstruction of the land vertebrate tree of life. This controversy has arisen after many different kinds and revisions of investigations of molecular and morphological data. Three main hypotheses of living sister-groups of turtles have resulted from them: all reptiles, crocodiles + birds or squamates + tuatara. Although embryology has played a major role in morphological studies of vertebrate phylogeny, data on developmental timing have never been examined to explore and test the alternative phylogenetic hypotheses. We conducted a comprehensive study of published and new embryological data comprising 15 turtle and eight tetrapod species belonging to other taxa, integrating for the first time data on the side-necked turtle clade.

Results

The timing of events in organogenesis of diverse character complexes in all body regions is not uniform across amniotes and can be analysed using a parsimony-based method. Changes in the relative timing of particular events diagnose many clades of amniotes and include a phylogenetic signal. A basal position of turtles to the living saurian clades is clearly supported by timing of organogenesis data.

Conclusion

The clear signal of a basal position of turtles provided by heterochronic data implies significant convergence in either molecular, adult morphological or developmental timing characters, as only one of the alternative solutions to the phylogenetic conundrum can be right. The development of a standard reference series of embryological events in amniotes as presented here should enable future improvements and expansion of sampling and thus the examination of other hypotheses about phylogeny and patterns of the evolution of land vertebrate development.