Since their discovery in the late 1970s, deep-sea hydrothermal systems have been considered as likely candidates for the origin and early evolution of life on Earth. However, while subsequent investigations have revealed a great diversity of modern deep-sea hydrothermal ecosystems, they have done little to shed light on the issues of the origin and early evolution of life, metabolism, cells, or communities. Phylogenetic, biochemical and geochemical clues all seem to point to the early evolution of hydrogenotrophic chemolithoautotrophy such as methanogenesis and sulfurreduction, thus pinpointing the availability of hydrogen as one of the key elements needed for the early evolution of earthly life. Hydrogen-driven, photosynthesis-independent communities are very rare on the contemporary Earth, however, being unambiguously found only in subsurface environments of H₂-dominated hydrothermal systems. Such systems have been termed hyperthermophilic subsurface lithoautotrophic microbial ecosystems (HyperSLiMEs) (Takai et al., 2004; Nealson et al., 2005). The supply of abundant hydrogen and available inorganic carbon sources to power such communities is most likely coupled to hydrothermal serpentinization of ultramafic rocks and input of magmatic volatiles, both of which are related to specific geological settings. We propose here, on the basis of findings in the modern Earth and implications for the deep-sea hydrothermal systems in the Archean Earth, that “Ultramafics-Hydrothermalism-Hydrogenesis-HyperSLiME”, a linkage we refer to as Ultra H³, provided a suitable habitat for the early microbial ecosystem on the Archean Earth.

Photosynthetic organisms have played a significant role as primary producers and ultimate sources of the atmospheric oxygen through geologic time. How they have evolved is one of the key questions in the study of the biological and environmental history of the Earth. Modern algal chloroplasts (plastids) are greatly diversified in morphology and pigmentation. Because the paleontological record can never be complete, a multidisciplinary approach is essential to reveal the pattern, timing, and mechanism of chloroplast evolution. Several independent lines of evidence show that all chloroplasts derived from a single endosymbiotic cyanobacterium and spread in different eukaryotic taxa via multiple secondary endosymbioses. With the advent of the genomic era, comparative genomics has been employed to reveal the course of their evolution. Yet, the study of non-model organisms remains important to understand how today's diverse life has evolved, such as in the case of uniquely pigmented prochlorophytes. Paleontological records may provide constraints on the timing of the primary and secondary endosymbiotic events.

This account firstly outlines the relationships between algal diversity and chloroplast acquisition through endosymbiosis. Secondly, it briefly reviews chloroplast diversity in dinoflagellates. Particular emphasis is placed on the evolutionary process in the small but interesting group of dinoflagellates that possess a diatom endosymbiont.

The genetic bases of skeletogenesis are expected to shed light on the origins of metazoan biomineralization. Here we review aspects of genetic machineries of invertebrate skeletogenesis, including regulatory genes involved in biomineralization as well, and with an enumerative reference to the genes encoding skeletal matrix proteins. The complete primary structure has been determined for a total of 77 skeletal matrix proteins in invertebrates representing five animal phyla. Presence of repeated sequences and prevalence of acidic proteins stand as common features among those proteins. Similarities are interpreted as convergence because these proteins are not similar at the primary structure level. C-type lectin-like domains are shared by the calcium carbonate skeletal matrix proteins of molluscs and deuterostomes. However, the important sites for carbohydrate binding are not conserved between these two groups. Several arthropod skeletal matrix proteins have the Rebers-Riddiford consensus sequence which is characteristic of non-calcified cuticular proteins of arthropods, indicating that these skeletal matrix proteins were recruited from the non-calcified cuticular proteins after arthropods diverged from other metazoan groups. Dermatopontin, a molluscan shell matrix protein, is also inferred to represent a cooption for biomineralization after molluscs diverged from other metazoan groups based on the molecular phylogemetic analysis. Those findings support the premise that the genetic machineries of biomineralization evolved independently many times after the divergence of metazoan phyla, and that some common genes that served for other functions have been coopted for biomineralization in various lineages.

Remarkable advances in developmental genetics in the past two decades allow us to approach the evolution of animal design by elucidating the molecular mechanisms underlying divergent body plans. The ancestry and evolution of segmented body plans in the bilaterians has been an active area of investigation in this field of study. Although segmentation mechanisms have been extensively studied for the fruit fly Drosophila melanogaster, Drosophila exhibits an evolutionarily derived mode of development, and molecular mechanisms underlying Drosophila segmentation may be unrepresentative for arthropods, even for insects. We have been studying the developmental system of the cricket, Gryllus bimaculatus, to understand more ancestral and general segmentation mechanisms for insects than those of Drosophila. In Gryllus, anterior segments are specified almost simultaneously, whereas posterior segments are specified sequentially in the extending posterior region. This mode of segmentation is general and probably ancestral for arthropods. Our RNA interference-based analyses of the functions and regulatory interactions of Gryllus orthologues of Drosophila segmentation genes have revealed surprisingly divergent aspects of the segmentation system in Gryllus in comparison with that of Drosophila. For example, the anteroposterior patterning in Gryllus is principally controlled by the caudal (cad) gene, probably without bicoid, unlike Drosophila. Comparisons of regulatory networks of segmentation genes between Gryllus and Drosophila suggest that regulatory interactions between the genes vary among insects, despite conservation of the network component genes. This implies that the molecular mechanisms of segmentation have changed dynamically during insect evolution, whereas the segmented body plan itself has been conserved. We also discuss evolution of developmental systems generating segment patterns in non-arthropod bilaterian animals.

Oceanic Anoxic Events (OAEs) mark the contemporaneous deposition of organic-rich marine sediments termed “black shales” in the wide areas of the oceans. An anoxic event that occurred at the Cenomanian-Turonian boundary, OAE-2, has been recognized as one of the largest events in the Cretaceous. Carbon isotopic compositions (δ¹³C) of sedimentary carbonate and organic matter exhibit a positive excursion across the OAE-2, reflecting an enhanced burial rate of ¹³C-depleted organic carbon during the event. Here we compile a spatiotemporal distribution of black shales on the basis of their onset timings relative to the δ¹³C excursion as a time-control reference, and discuss the “spreading patterns” of black shale deposition. The patterns suggest that the deposition of black shales started from marginal regions of the southern North Atlantic and the Western Interior Seaway in North America, and spread to the northern North Atlantic and Tethys Sea. Strangely, the black shales whose onset corresponds to that of the δ¹³C excursion have not been found in many locations. Furthermore, extensive deposition of black shales in the Tethys and some sites in the North Atlantic occurred significantly after the major shift of the δ¹³C excursion. Sediments in the largely unexplored Pacific basin may be the missing link in the temporal relationship between the black shale deposition and the isotopic excursion.

Corals are widely distributed throughout a long stretch of geological time and can provide high-resolution histories of climatic variabilities in the tropics, which play a key role in understanding the Earth's climate system. Geochemical approaches to corals have been widely used for reconstructing palaeoclimates because the geochemistry of the skeleton is believed to vary as a function of several environmental conditions. However, large variations that cannot be ascribed to a single environmental factor have been observed among and/or within calibrations of coral-based proxies. Two main unsolved factors could lead to these large discrepancies: unexpected environmental changes in reefs and unknown biological processes occurring at coral biomineralization sites. In this review, we show the recent progress in dealing with this question by application of coral culture technique and micro analytical methods to skeletal geochemistry in corals and discuss on how the degree of geochemical variation could be affected by environmental changes and how by biological processes during the skeleton's calcification. The next challenge will be to perform high-resolution analysis on cultured corals growing under controlled and/or constant environmental conditions. Such efforts hold the promise of yielding important new insights into the various biomineralization processes that may affect the chemical and isotopic composition of the skeletons, with the goal of understanding how environmental changes express themselves in geochemical variability.

Computer simulations of ecosystems are useful for revealing in detail the ecological processes concerned with major bioevents. Unlike empirical approaches, theoretical models allow us to see virtual evolutionary changes in interspecific interactions in a much shorter time as compared with evolutionary experiments. Some recent ecosystem models succeeded in constructing hypothetical ecosystems with high species diversity by introducing low connectance and gradual evolution. Some of these hypothetical ecosystems had similar properties to real ecosystems. Some models incorporated biologically meaningful rules for constructing interspecific interactions, whereas others did not. Both types of model are complementary to each other: which to choose depends on the purpose of the study. Most of the former type of model focused on incorporating biologically realistic processes. They do not aim to mimic the topological features of real ecosystems. It is quite natural that such models did not reproduce ecosystems similar to real ecosystems. Therefore, the reality of such models should be tested not only by using the topology of the ecosystem but also by using parameters which are suitable for the purpose of the models.