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opencc-zeroAug 2022View details →

Evolutionary changes in the chromatin landscape contribute to reorganization of a developmental gene network during rapid life history evolution in sea urchins

Chromatin configuration is highly dynamic during embryonic development in animals, exerting an important point of control in transcriptional regulation. Yet there exists remarkably little information about the role of evolutionary changes in chromatin configuration to the evolution of gene expression and organismal traits. Genome-wide assays of chromatin configuration, coupled with whole-genome alignments, can help address this gap in knowledge in several ways. In this study, we present a comparative analysis of regulatory element sequences and accessibility throughout embryogenesis in three sea urchin species with divergent life histories: a lecithotroph Heliocidaris erythrogramma, a closely related planktotroph H. tuberculata, and a distantly related planktotroph Lytechinus variegatus. We identified distinct epigenetic and mutational signatures of evolutionary modifications to the function of putative cis-regulatory elements in H. erythrogramma that have accumulated non-uniformly throughout the genome, suggesting selection, rather than drift, underlies many modifications associated with the derived life history. Specifically, regulatory elements composing the sea urchin developmental gene regulatory network are enriched for signatures of positive selection and accessibility changes which may function to alter binding affinity and access of developmental transcription factors to these sites. Furthermore, regulatory element changes often correlate with divergent expression patterns of genes involved in cell type specification, morphogenesis, and development of other derived traits, suggesting these evolutionary modifications have been consequential for phenotypic evolution in H. erythrogramma. Collectively, our results demonstrate that selective pressures imposed by changes in developmental life history rapidly reshape the cis-regulatory landscape of core developmental genes to generate novel traits and embryonic programs.

Figure 3 in Covering behaviour in the sea urchin Pseudechinus magellanicus (Temnopleuridae) in central Patagonia, Argentina

Figure 3. Non-metric multidimensional scaling (nMDS) and polygons on SØrensen similarity matrix (qualitative) of coverage items used by Pseudechinus magellanicus across different sites (A) and depths (B). PA: Pasto Amarillo; LT: La Tranquera; Km3: Kilómetro 3; LwMT: Low midlittoral tidepools; IFT: Infralittoral tidepools.

Figure 7 in Covering behaviour in the sea urchin Pseudechinus magellanicus (Temnopleuridae) in central Patagonia, Argentina

Figure 7. Relation between the areas of items available in the environment (supply) and those used by Pseudechinus magellanicus for covering purposes. (A) Frequency distribution and box plot; (B) categorical analysis.

Figure 4 in Covering behaviour in the sea urchin Pseudechinus magellanicus (Temnopleuridae) in central Patagonia, Argentina

Figure 4. Proportion of sea urchins with varying degrees of surface coverage in two size classes (n = 40 and 50 for small and large, respectively).

Figure 2 in Covering behaviour in the sea urchin Pseudechinus magellanicus (Temnopleuridae) in central Patagonia, Argentina

Figure 2. Covering behaviour of Pseudechinus magellanicus showing varying degrees of coverage in central Patagonia, Argentina.

Figure 6 in Covering behaviour in the sea urchin Pseudechinus magellanicus (Temnopleuridae) in central Patagonia, Argentina

Figure 6. Proportion of sea urchins with varying degrees of surface coverage in relation to proximity to sandy beaches at infralittoral tidepools, one with higher fine sand contribution (proximal; n = 29) and another with lower sand input (distant; n = 46).

Figure 5 in Covering behaviour in the sea urchin Pseudechinus magellanicus (Temnopleuridae) in central Patagonia, Argentina

Figure 5. Proportion of sea urchins with varying degrees of surface coverage along a coastal depth gradient at Central Patagonia, Argentina. LwMT: low midlittoral tidepools (n = 49); IFT: infralittoral tidepools (n = 119); depth 5–7 m (n = 57); depth 10–12 m (n = 90).

opencc-zeroDec 2011View details →

Data from: Differences in the regulation of growth and biomineralization genes revealed through long-term common garden acclimation and experimental genomics in the purple sea urchin

Across heterogeneous landscapes, populations may have adaptive differences in gene regulation that adjust their physiologies to match local environments. Such differences could have origins in acclimation or in genetically fixed variation between habitats. Here we use common garden experiments to evaluate differences in gene expression between populations of the purple sea urchin, Strongylocentrotus purpuratus, spanning 1700 km and average temperature differences of 5 °C to 8 °C. Across expression profiles from 18,883 genes after three years of common conditions, we find highly correlated expression patterns (Pearson's r = 0.992) among most genes. However, sixty-six genes were differentially expressed, including many ribosomal protein and biomineralization genes, all of which had higher expression in urchins originally from the southern population. Gene function analyses revealed slight but pervasive expression differences in genes related to ribosomal function, metabolism, transport, "bone" development, and response to stimuli. In accord with gene expression patterns, a post-hoc spine re-growth experiment revealed that urchins of southern origin re-grew spines at a faster rate than northern urchins. These results suggest that there may be genetically controlled, potentially adaptive differences in gene regulation across habitats and that gene expression differences may be under strong enough selection to overcome high dispersal-mediated gene flow in this marine species.

opencc-zeroDec 2012View details →

Data from: Modeling of the larval response of green sea urchins to thermal stratification using a random walk approach

Larval transport in the ocean can be affected by their vertical position in the water column. In biophysical models that are often used to predict larval horizontal dispersal, generally larval vertical positions are either ignored or incorporated as static parameters. Here, we evaluate the ability of one dimensional random walk based model to predict larval vertical distribution of Strongylocentrotus droebachiensis in response to thermal stratification. Vertical swimming velocities were recorded at various temperatures and used to parameterize the model. Data from a previous laboratory study on the effects of thermal stratification on larval vertical distribution of S. droebachiensis were compared to the model results to evaluate the predictive ability of the model. The model predicts general trends in vertical distribution fairly well, but has a systematic bias which can be explained by un-quantified larval behaviors at the boundaries of the experimental water column. Overall, our behavioral model successfully reproduces the mechanism which regulates larval vertical distribution in response to thermal structure. Collectively, the findings suggest that simple behavioral models parameterized using simple lab experiments can prove useful in estimating the vertical distributions of invertebrate larvae in the laboratory and likely in the ocean. Such models can then be linked to bio-physical models to more accurately predict larval dispersal.

opencc-zeroDec 2018View details →

Data from: Functional consequences of morphologically plastic jaws in juvenile purple sea urchins

Morphological plasticity is a critical mechanism that animals use to cope with variation in resource availability. During periods of food scarcity, sea urchins demonstrate an increase in jaw length relative to test diameter. This trait is thought to be reversible and adaptive by yielding an increase in feeding efficiency. We directly test the hypotheses that (1) there are reversible shifts in jaw length to test diameter ratios with food abundance in individual urchins, and (2) these shifts alter feeding efficiency. Purple sea urchins, Strongylocentrotus purpuratus, were placed in either high or low food treatments for 3 months, after which treatments were switched for 2 additional months. Measurements of jaw length to test diameter ratios were significantly higher in low compared to high food urchins, but this was due to test growth in the high food treatments. Ratios of low food urchins did not change following a switch to high food conditions, indicating that this trait is not reversible. Relatively longer jaws were also not correlated with increased feeding efficiency. We argue that jaw length plasticity is not adaptive and is simply a consequence of exposure to high food availability, as both jaw and test growth halt when food is scarce.

opencc-zeroJul 2021View details →

Unraveling the predictive role of temperature in the gut microbiota of the sea urchin Echinometra sp. EZ across spatial and temporal gradients

Shifts in microbial communities represent a rapid response mechanism for host organisms to respond to changes in environmental conditions. Therefore, they are likely to be important in assisting the acclimatization of hosts to seasonal temperature changes as well as to variation in temperatures across a species' range. The Persian/Arabian Gulf is the world's warmest sea, with large seasonal fluctuations in temperature (20℃ - 37℃) and is connected to the Gulf of Oman which experiences more typical oceanic conditions (<32℃ in the summer). This system is an informative model for understanding how symbiotic microbial assemblages respond to thermal variation across temporal and spatial scales. Here, we elucidate the role of temperature on the microbial gut community of the sea urchin Echinometra sp. EZ and identify microbial taxa that are tightly correlated with the thermal environment. We generated two independent datasets with a high degree of geographic and temporal resolution. The results show that microbial communities vary across thermally variable habitats, display temporal shifts that correlate with temperature, and can become more disperse as temperatures rise. The relative abundances of several ASVs significantly correlate with temperature in both independent datasets despite the >300 km distance between the furthest sites and the extreme seasonal variations. Notably, over 50% of the temperature predictive ASVs identified from the two datasets belonged to the family Vibrionaceae. Together, our results identify temperature as a robust predictor of community-level variation and highlight specific microbial taxa putatively involved in the response to thermal environment.

ClinicalTrials.gov32/100

COVID-19 Sequelae: Treatment and Monitoring. A Dietary Supplement Based on Sea Urchin Eggs With Echinochroma A

ClinicalTrials.gov study NCT05531019. IPD Sharing: YES. Countries: 1. Publications: 11.

controlledIPD-YESFeb 2026View details →