Inferring Tunicate Relationships And The Evolution Of The Tunicate Hox Cluster With The Genome Of Corella Inflata

Tunicates, the closest living relatives of vertebrates, have served as a foundational model of early embryonic development for decades. Comparative studies of tunicate phylogeny and genome evolution provide a critical framework for analyzing chordate diversification and the emergence of vertebrates. Towards this goal, we sequenced the genome of Corella inflata (Ascidiacea, Phlebobranchia), so named for the capacity to brood self-fertilized embryos in a modified, “inflated” atrial chamber. Combining the new genome sequence for Co. inflata with publicly available tunicate data, we estimated a tunicate species phylogeny, reconstructed the ancestral Hox gene cluster at important nodes in the tunicate tree, and compared patterns of gene loss between Co. inflata and Ciona robusta, the prevailing tunicate model species. Our maximum-likelihood and Bayesian trees estimated from a concatenated 210-gene matrix were largely concordant and showed that Aplousobranchia was nested within a paraphyletic Phlebobranchia. We demonstrated that this relationship is not an artifact due to compositional heterogeneity, as had been suggested by previous studies. In addition, within Thaliacea, we recovered Doliolida as sister to the clade containing Salpida and Pyrosomatida. The Co. inflata genome provides increased resolution of the ancestral Hox clusters of key tunicate nodes, therefore expanding our understanding of the evolution of this cluster and its potential impact on tunicate morphological diversity. Our analyses of other gene families revealed that several cardiovascular associated genes (e.g., BMP10, SCL2A12, and PDE2a) absent from Ci. robusta are present in Co. inflata. Taken together, our results help clarify tunicate relationships and the genomic content of key ancestral nodes within this phylogeny, providing critical insights into tunicate evolution

Variable Levels Of Drift In Tunicate Cardiopharyngeal Gene Regulatory Elements

Background: Mutations in gene regulatory networks often lead to genetic divergence without impacting gene expression or developmental patterning. The rules governing this process of developmental systems drift, including the variable impact of selective constraints on different nodes in a gene regulatory network, remain poorly delineated. Results: Here we examine developmental systems drift within the cardiopharyngeal gene regulatory networks of two tunicate species, Corella inflata and Ciona robusta. Cross-species analysis of regulatory elements suggests that trans-regulatory architecture is largely conserved between these highly divergent species. In contrast, cis-regulatory elements within this network exhibit distinct levels of conservation. In particular, while most of the regulatory elements we analyzed showed extensive rearrangements of functional binding sites, the enhancer for the cardiopharyngeal transcription factor FoxF is remarkably well-conserved. Even minor alterations in spacing between binding sites lead to loss of FoxF enhancer function, suggesting that bound trans-factors form position-dependent complexes. Conclusions: Our findings reveal heterogeneous levels of divergence across cardiopharyngeal cis-regulatory elements. These distinct levels of divergence presumably reflect constraints that are not clearly associated with gene function or position within the regulatory network. Thus, levels of cis-regulatory divergence or drift appear to be governed by distinct structural constraints that will be difficult to predict based on network architecture

Severity of Depressive Symptoms and Accuracy of Dietary Reporting among Obese Women with Major Depressive Disorder Seeking Weight Loss Treatment

An elevation in symptoms of depression has previously been associated with greater accuracy of reported dietary intake, however this association has not been investigated among individuals with a diagnosis of major depressive disorder. The purpose of this study was to investigate reporting accuracy of dietary intake among a group of women with major depressive disorder in order to determine if reporting accuracy is similarly associated with depressive symptoms among depressed women. Reporting accuracy of dietary intake was calculated based on three 24-hour phone-delivered dietary recalls from the baseline phase of a randomized trial of weight loss treatment for 161 obese women with major depressive disorder. Regression models indicated that higher severity of depressive symptoms was associated with greater reporting accuracy, even when controlling for other factors traditionally associated with reporting accuracy (coefficient  =  0.01 95% CI = 0.01 – 0.02). Seventeen percent of the sample was classified as low energy reporters. Reporting accuracy of dietary intake increases along with depressive symptoms, even among individuals with major depressive disorder. These results suggest that any study investigating associations between diet quality and depression should also include an index of reporting accuracy of dietary intake as accuracy varies with the severity of depressive symptoms

Genetic Assessment of Connectivity in the Common Reef Sponge, Callyspongia vaginalis (Demospongiae: Haplosclerida) Reveals High Population Structure Along the Florida Reef Tract

The genetic population structure of the common branching vase sponge, Callyspongia vaginalis, was determined along the entire length (465 km) of the Florida reef system from Palm Beach to the Dry Tortugas based on sequences of the mitochondrial cytochrome c oxidase subunit 1 (COI) gene. Populations of C. vaginalis were highly structured (overall ϕST = 0.33), in some cases over distances as small as tens of kilometers. However, nonsignificant pairwise ϕST values were also found between a few relatively distant sampling sites suggesting that some long distance larval dispersal may occur via ocean currents or transport in sponge fragments along continuous, shallow coastlines. Indeed, sufficient gene flow appears to occur along the Florida reef tract to obscure a signal of isolation by distance, but not to homogenize COI haplotype frequencies. The strong genetic differentiation among most of the sampling locations suggests that recruitment in this species is largely local source-driven, pointing to the importance of further elucidating general connectivity patterns along the Florida reef tract to guide the spatial scale of management efforts

Comparative Phylogeography, Dispersal Strategy, and Biodiversity in Three Commensal Invertebrates and Their Host Sponge

Effective spatial management of coral reefs and marine protected area design require an understanding of genetic connectivity and biodiversity among reefs. We report a comparative analysis of connectivity (gene flow) in three commensal invertebrates and their host sponge, all of which display contrasting reproductive dispersal strategies: two spawners (the brittle star Ophiothrix lineata and the branching vase sponge Callyspongia vaginalis) and two brooders (the amphipods Leucothoe ashleyae and Leucothoe kensleyi). Mitochondrial DNA sequence variation was used to infer connectivity along 355km of the SE Florida coastline and among Caribbean islands. C. vaginalis showed the highest genetic structuring along the Florida coastline whereas the amphipods showed surprisingly high levels of gene flow despite a lack of pelagic larvae. In contrast to the brooders, both spawning species showed a strong pattern of genetic isolation by distance, and a Bayesian analysis of migration revealed a southerly bias to gene flow along the Florida coastline for the brittle star counter to the northerly flow of the Florida Current. Results among Caribbean and Florida locations were opposite to those obtained along the Florida coastline, as connectivity for all species was highly restricted. Furthermore, both amphipod species are divided into genetically highly divergent lineages across the Caribbean, suggestive of multiple cryptic species. Our results show that inferring connectivity based simply on reproductive dispersal strategies may be misleading, and highlight the need to integrate morphological taxonomy with genetic analysis to reveal the full extent of coral reef biodiversity

Data from: Adaptation to heat stress reduces phenotypic and transcriptional plasticity in a marine copepod

Organisms may respond to changing environments through phenotypic plasticity or adaptive evolution. These two processes are not mutually exclusive and may either dampen or strengthen each other's effects, depending on the genetic correlation between trait values and the slopes of their norms of reaction. To examine the effect of adaptation to heat stress on the plasticity of heat tolerance, we hybridized populations of the crustacean Tigriopus californicus that show divergent phenotypes for heat tolerance. We then selected for increased heat tolerance in hybrids and measured heat tolerance and the phenotypic plasticity of heat tolerance in both selected lines and unselected controls. To test whether the changes in phenotypic plasticity were associated with changes in the plasticity of gene expression, we also sequenced transcriptomes of selected and unselected lines, both under heat shock and at ambient temperatures. We observed increased heat tolerance in selected lines, but also lower phenotypic and transcriptional plasticity in response to heat stress. The plastic response to heat stress was highly enriched for hydrolytic and catalytic activities, suggesting a prominent role for degradation of misfolded proteins. Our findings have important implications for biological responses to climate change: if adaptation to environmental stress reduces plasticity, then plasticity and adaptive evolution will make overlapping, rather than additive contributions to buffering populations from environmental change

Maximum likelihood tree Echinometra species COI

Eight Echinometra COI sequences were included in our Maximum likelihood tree (ML); E. sp. C, E. oblonga, E. sp. A, E. mathaei, E. sp. EZ, our sample, the COI sequence extracted from the published E. mathaei mitogenome (denoted with an asterisk), and E. lucunter as an outgroup. The published E. mathaei mitogenome COI sequence is most closely grouped with the E. sp. EZ sequences. In order to generate the ML tree, we used a MAFFT alignment and an E-INS-i algorithm to align COI sequences (441 column nucleotide alignment) in Geneious v11.1.4. MEGA v7.0.21 was used to determine that the best fit model for the ML tree construction was K2+G. The ML tree was constructed in the PhyML v.3.0 plugin in Geneious v11.1.4. The numbers above the branches specify bootstrap percentages (1,000 replicates) and accession numbers are to the right of the species name. The sequence alignment used to generate this tree is also included in this data package submission

SNP table

Table includes SNPs that differentiate our Echinometra sp. EZ mitogenome from the published Echinometra mathaei mitogenome. Table includes polymorphism type, the base pair found in each respective mitogenome for that SNP position, the numerical position of the SNP in the mitogenome, and mitochondrial region the SNP is found in