As a result of climate change, the Mediterranean Sea has been exposed to an increase in frequency and intensity of marine heat waves in the last decades, some of which caused mass mortality events of benthic invertebrates, including sponges. Sponges are an important component of benthic ecosystems and can be the dominant group in some rocky shallow-water areas in the Mediterranean Sea. In this study, we exposed the common shallow-water Mediterranean sponge Chondrilla nucula (Demospongiae: Chondrillidae) to six different temperatures for 24 h, ranging from temperatures experienced in the field during the year (15, 19, 22, 26, 28 °C) and above normal temperatures (32 °C) and metabolic (respiration rate) and behavioural (clearance rate) were measured. Both respiration and clearance rates were affected by temperature. Respiration rates increased at higher temperatures but were similar between 26 and 32 °C treatments. Clearance rates decreased at temperatures > 26 °C, indicating a drop in food intake that was not reflected by respiration rates. This decline in feeding, while maintaining high respiration rates, may indicate a negative energy balance that could affect this species under chronic or repeated thermal stress exposure. C. nucula will probably be a vulnerable species under climate change conditions, affecting its metabolic performance, ecological functioning and the ecosystem services it provides.

The most widely accepted scientific theory for the origin of life on Earth is that prokaryotic microbes evolved from simple organic compounds in seawater under anoxic conditions. For about 1 billion years thereafter, these microbes consumed the same dissolved organic matter (DOM) from which they had evolved before scarcity of DOM forced the evolution of cyanobacterial photosynthesis followed by eukaryosis. Could the more efficient consumption of DOM have also stimulated the subsequent origin of multicellular animal life? In this report, we synthesize past and recent evidence to propose the “DOM uptake hypothesis” for the origin of metazoans. A choanoflagellate-like protozoan was the likely ancestor of the first sponge-like metazoan to evolve on Earth. Choanoflagellates have outwardly facing flagellae that are subject to viscous water movement, while sponges have choanocytes in chambers with flagellae directed to pump water with greater fluidity across an aquiferous system with a huge cellular surface area. While generally considered particle feeders, both choanoflagellates and sponges absorb DOM, with some sponges relying on DOM for as much as 90% of their diet. We propose that the earliest metazoans may have evolved to survive the dire nutritional conditions of the Cryogenian “snow-ball Earth” period (~700 million years ago) by developing a body plan with the enhanced ability to absorb low concentrations of DOM in seawater from sources such as the viral lysis of microbes, exudates of benthic stromatolites, or refractory DOM compounds. Additionally, species of extant sponges that have a high abundance of microbes living in their bodies consume the greatest amounts of DOM, suggesting that the DOM uptake hypothesis may also be dependent on microbial symbiosis.

Here, we critically evaluate the communication and integrative mechanisms in ctenophores or comb jellies, the descendants of the earliest animal lineage. Ctenophores convergently evolved their neuro-muscular systems compared to other animals. Besides the canonical neural organization with distinct synapses, recent 3D electron microscopy reconstruction revealed unique syncytial-type connectivity in some neuronal populations, providing additional support for the independent origins of neurons in ctenophores. Furthermore, it was proposed that non-synaptic transmission is the distinct characteristic of ctenophores, in contrast to other metazoans and Cajal’s neuronal doctrine, highlighting Golgi’s reticular theory. However, the astonishing diversity and higher information capacity of classical synapses and volume transmission indicate that chemical signaling is the hallmark of neural and other integrative systems regardless of their origins.

Phylogenomics, the use of large datasets to examine phylogeny, has revolutionized the study of evolutionary relationships. However, genome-scale data have not been able to resolve all relationships in the tree of life; this could reflect, at least in part, the poor-fit of the models used to analyze heterogeneous datasets. Some of the heterogeneity may reflect the different patterns of selection on proteins based on their structures. To test that hypothesis, we developed a pipeline to divide phylogenomic protein datasets into subsets based on secondary structure and relative solvent accessibility. We then tested whether amino acids in different structural environments had distinct signals for the topology of the deepest branches in the metazoan tree. The most striking difference in phylogenetic signal reflected relative solvent accessibility; analyses of exposed sites (on the surface of proteins) yielded a tree that placed ctenophores sister to all other animals whereas sites buried inside proteins yielded a tree with a sponge-ctenophore clade. These differences in phylogenetic signal were not ameliorated when we repeated our analyses using the CAT model, a mixture model that is often used for analyses of protein datasets. In fact, the heterogeneous CAT model resulted in several rearrangements that are unlikely to represent evolutionary history. However, analyses conducted after recoding amino acids to limit the impact of deviations from compositional stationarity increased the congruence in the estimates of phylogeny for exposed and buried sites; after recoding amino acids both trees supported placement of ctenophores sister to all other animals. These results provide striking evidence that it is necessary to achieve a better understanding of the constraints due to protein structure to improve phylogenetic estimation.

Despite the long history of using protein sequences to infer the tree of life the potential for different parts of protein structures to retain historical signal remains unclear. We propose that it might be possible to improve analyses of phylogenomic datasets by incorporating information about protein structure; we test this idea using the position of the root of Metazoa (animals) as a model system. We examined the distribution of “strongly decisive” sites (alignment positions that support a specific tree topology) in a dataset comprising >1,500 proteins and almost 100 taxa. The proportion of each class of strongly decisive sites in different structural environments was very sensitive to the model used to analyze the data when a limited number of taxa were used but they were stable when taxa were added. As long as enough taxa were analyzed, sites in all structural environments supported the same topology (ctenophores sister to other animals) regardless of whether standard tree searches or decisive sites were used to select the optimal tree. However, the use of decisive sites revealed a difference between the support for minority topologies for sites in different structural environments; buried sites and sites in sheet and coil environments exhibited equal support for the minority topologies whereas solvent exposed and helix sites had unequal numbers of sites supporting the minority topologies. Given the plausible trees equal support for minority topologies is consistent with discordance among gene trees, making it possible the relatively slowly evolving buried (and sheet and coil) sites are giving an accurate picture of the true species tree as well as the amount of conflict among gene trees. Alternatively, the apparent support could reflect currently uncharacterized processes of molecular evolution. Regardless, it is clear that analyses of the deepest branches in the animal tree of life using sites in different structural environments are associated with a subtle data type effect that results in distinct phylogenetic signals.