Evolution Of Calcification Research Articles

Variation in calcification of Reticulofenestra coccoliths over the Oligocene–Early Miocene

Abstract. Coccolithophores are calcifying marine phytoplankton whose intracellularly produced calcite plates, coccoliths, have been the dominant source of calcium carbonate in open-ocean settings since the Cretaceous. An open question is whether their calcification has been affected by changing environmental conditions over geological timescales such as variations in the ocean carbon system. Previous methods using circular polarized light microscopy allowed for only the thickness of small coccoliths thinner than 1.5 µm to be quantified, but prior to the Pliocene, a significant fraction of the coccoliths exceeded this thickness and have not been quantifiable. Here, we implement a new approach for calibration of circular polarized light microscopy enabling us to quantify coccoliths which feature calcite up to 3 µm thick. We apply this technique to evaluate the evolution of calcification in the Reticulofenestra from the early Oligocene to Early Miocene in exceptionally well-preserved sediments from the Newfoundland margin. Through this time interval, coccolith thickness and the scale-invariant shape factor kse vary by about 20 % around the mean thickness of 0.37 µm and mean kse of 0.16. Lower shape factors characterize samples with a higher relative abundance of dissolution-resistant nannoliths, suggesting that dissolution may contribute to thinning of placoliths. We therefore define temporal trends in calcification only in samples in which the assemblage suggests minimal dissolution. The lowest kse characterizes the middle Oligocene, and the highest kse around 18 Ma is in the Early Miocene. High ocean dissolved inorganic carbon (DIC) concentrations have been proposed for this period of the Miocene and may be one factor contributing to high coccolith kse.

Evolutionary Rates in the Haptophyta: Exploring Molecular and Phenotypic Diversity

Haptophytes are photosynthetic protists found in both freshwater and marine environments with an origin possibly dating back to the Neoproterozoic era. The most recent molecular phylogeny reveals several haptophyte “mystery clades” that await morphological verification, but it is otherwise highly consistent with morphology-based phylogenies, including that of the coccolithophores (calcifying haptophytes). The fossil coccolith record offers unique insights into extinct lineages, including the adaptive radiations that produced extant descendant species. By combining molecular data of extant coccolithophores and phenotype-based studies of their ancestral lineages, it has become possible to probe the modes and rates of speciation in more detail, although this approach is still limited to only few taxa because of the lack of whole-genome datasets. The evolution of calcification likely involved several steps, but its origin can be traced back to an early association with organic scales typical for all haptophytes. Other key haptophyte traits, including the haplo-diplontic life cycle, are herein mapped upon the coccolithophorid phylogeny to help navigate a discussion of their ecological benefits and trade-offs in a rapidly changing ocean.

The Evolution of Calcification in Reef-Building Corals.

Corals build the structural foundation of coral reefs, one of the most diverse and productive ecosystems on our planet. Although the process of coral calcification that allows corals to build these immense structures has been extensively investigated, we still know little about the evolutionary processes that allowed the soft-bodied ancestor of corals to become the ecosystem builders they are today. Using a combination of phylogenomics, proteomics, and immunohistochemistry, we show that scleractinian corals likely acquired the ability to calcify sometime between ∼308 and ∼265 Ma through a combination of lineage-specific gene duplications and the co-option of existing genes to the calcification process. Our results suggest that coral calcification did not require extensive evolutionary changes, but rather few coral-specific gene duplications and a series of small, gradual optimizations of ancestral proteins and their co-option to the calcification process.

Draft genomes of the corallimorpharians Amplexidiscus fenestrafer and Discosoma sp.

Corallimorpharia are the closest noncalcifying relatives of reef-building corals. Aside from their popularity among aquarium hobbyists, their evolutionary position between the Actiniaria (sea anemones) and the Scleractinia (hard corals) makes them ideal candidates for comparative studies aiming at understanding the evolution of hexacorallian orders in general and reef-building corals in particular. Here we have sequenced and assembled two draft genomes for the Corallimorpharia species Amplexidiscus fenestrafer and Discosoma sp. The draft genomes encompass 370 and 445Mbp, respectively, and encode for 21,372 and 23,199 genes. To facilitate future studies using these resources, we provide annotations for the predicted gene models-not only at gene level, by annotating gene models with the function of the best-matching homologue, and GO terms when available; but also at protein domain level, where gene function can be better verified through the conservation of the sequence and order of protein domains. Further, we provide an online platform (http://corallimorpharia.reefgenomics.org), which includes a blast interface and a genome browser to facilitate the use of these resources. We believe that these two genomes are important resources for future studies on hexacorallian systematics and the evolutionary basis of their specific traits such as the symbiotic relationship with dinoflagellates of the genus Symbiodinium or the evolution of calcification in reef-building corals.

The Skeletal Proteome of the Coral Acropora millepora: The Evolution of Calcification by Co-Option and Domain Shuffling

In corals, biocalcification is a major function that may be drastically affected by ocean acidification (OA). Scleractinian corals grow by building up aragonitic exoskeletons that provide support and protection for soft tissues. Although this process has been extensively studied, the molecular basis of biocalcification is poorly understood. Notably lacking is a comprehensive catalog of the skeleton-occluded proteins—the skeletal organic matrix proteins (SOMPs) that are thought to regulate the mineral deposition. Using a combination of proteomics and transcriptomics, we report the first survey of such proteins in the staghorn coral Acropora millepora. The organic matrix (OM) extracted from the coral skeleton was analyzed by mass spectrometry and bioinformatics, enabling the identification of 36 SOMPs. These results provide novel insights into the molecular basis of coral calcification and the macroevolution of metazoan calcifying systems, whereas establishing a platform for studying the impact of OA at molecular level. Besides secreted proteins, extracellular regions of transmembrane proteins are also present, suggesting a close control of aragonite deposition by the calicoblastic epithelium. In addition to the expected SOMPs (Asp/Glu-rich, galaxins), the skeletal repertoire included several proteins containing known extracellular matrix domains. From an evolutionary perspective, the number of coral-specific proteins is low, many SOMPs having counterparts in the noncalcifying cnidarians. Extending the comparison with the skeletal OM proteomes of other metazoans allowed the identification of a pool of functional domains shared between phyla. These data suggest that co-option and domain shuffling may be general mechanisms by which the trait of calcification has evolved.