Molecular fossils within bitumens and kerogens from the ~ 1 Ga Lakhanda Lagerstätte (Siberia, Russia) and their significance for understanding early eukaryote evolution

The emergence and diversification of eukaryotes during the Proterozoic is one of the most fundamental evolutionary developments in Earth’s history. The ca. 1-billion-year-old Lakhanda Lagerstätte (Siberia, Russia) contains a wealth of eukaryotic body fossils and offers an important glimpse into their ecosystem. Seeking to complement the paleontological record of this remarkable lagerstätte, we here explored information encoded within sedimentary organic matter (total organic carbon = 0.01–1.27 wt.%). Major emphasis was placed on sedimentary hydrocarbons preserved within bitumens and kerogens, including molecular fossils (or organic biomarkers) that are specific to bacteria and eukaryotes (i.e. hopanes and regular steranes, respectively). Programmed pyrolysis and molecular organic geochemistry suggest that the organic matter in the analyzed samples is about peak oil window maturity and thus sufficiently well preserved for detailed molecular fossil studies that include hopanes and steranes. Together with petrographic evidence as well as compositional similarities of the bitumens and corresponding kerogens, the consistency of different independent maturity parameters establishes that sedimentary hydrocarbons are indigenous and syngenetic to the host rock. The possible presence of trace amounts of hopanes and absence of steranes in samples that are sufficiently well preserved to retain both types of compounds evidences an environment dominated by anaerobic bacteria with no or very little inputs by eukaryotes. In concert with the paleontological record of the Lakhanda Lagerstätte, our study adds to the view that eukaryotes were present but not significant in Mesoproterozoic ecosystems.

Molecular fossils illuminate the evolution of retroviruses following a macroevolutionary transition from land to water

The ancestor of cetaceans underwent a macroevolutionary transition from land to water early in the Eocene Period >50 million years ago. However, little is known about how diverse retroviruses evolved during this shift from terrestrial to aquatic environments. Did retroviruses transition into water accompanying their hosts? Did retroviruses infect cetaceans through cross-species transmission after cetaceans invaded the aquatic environments? Endogenous retroviruses (ERVs) provide important molecular fossils for tracing the evolution of retroviruses during this macroevolutionary transition. Here, we use a phylogenomic approach to study the origin and evolution of ERVs in cetaceans. We identify a total of 8,724 ERVs within the genomes of 25 cetaceans, and phylogenetic analyses suggest these ERVs cluster into 315 independent lineages, each of which represents one or more independent endogenization events. We find that cetacean ERVs originated through two possible routes. 298 ERV lineages may derive from retrovirus endogenization that occurred before or during the transition from land to water of cetaceans, and most of these cetacean ERVs were reaching evolutionary dead-ends. 17 ERV lineages are likely to arise from independent retrovirus endogenization events that occurred after the split of mysticetes and odontocetes, indicating that diverse retroviruses infected cetaceans through cross-species transmission from non-cetacean mammals after the transition to aquatic life of cetaceans. Both integration time and synteny analyses support the recent or ongoing activity of multiple retroviral lineages in cetaceans, some of which proliferated into hundreds of copies within the host genomes. Although ERVs only recorded a proportion of past retroviral infections, our findings illuminate the complex evolution of retroviruses during one of the most marked macroevolutionary transitions in vertebrate history.

Formation, diagenesis and fauna of cold seep carbonates from the Miocene Taishu Group of Tsushima (Japan)

The studied seep carbonates from Tsushima, Japan, are embedded within marine siliciclastics of the lower Miocene Taishu Group and represent the earliest evidence of hydrocarbon seepage in the Sea of Japan. In contrast to Miocene and Pliocene examples from Honshu, which are often found above anticlines, the seeps from Tsushima formed within a pull-apart basin before major anticlines had formed. The three carbonates from Fukuzaki, Kanoura and Tanohama are composed chiefly of calcite, with significant admixture of ankerite only at Kanoura. The stable carbon isotope composition of calcites (δ13C as low as −40.2 ‰ VPDB for Fukuzaki, −41.8 ‰ VPDB for Kanoura, and −52.8 ‰ VPDB for Tanohama) indicate methanogenic origin of the carbonates. Textures of these deposits, including radiaxial and yellow cements, are indicative of formation at a methane seep. The stable oxygen isotope composition of calcites (δ18O values as low as −14.4 ‰ VPDB for Fukuzaki, −14.5 ‰ VPDB for Kanoura and −13.9 ‰ VPDB for Tanohama) indicate that they were influenced by burial fluids. Burial diagenesis is also indicated by the stable isotopic compositions of ankerite (δ13C ranging from −19.1 ‰ to −7.1 ‰ VPDB, δ18O from −11.1 ‰ to −9.7 ‰ VPDB). Molecular fossils from Tanohama comprise n-alkanes with short-chain predominance, interpreted to have formed due to thermal cracking of organic matter. The carbonates yield a chemosynthesis-based community comprising vesicomyids Pleurophopsis chitanii, P. cf. hamuroi, the bathymodiolin ‘Bathymodiolus’ akanudaensis, the lucinid Lucinoma sp. and the provannid Provanna? sp., which have never been hitherto identified. ‘Bathymodiolus’ akanudaensis, Lucinoma sp. and Provanna? sp. are the oldest records of these taxa in the Sea of Japan.

Molecular fossils inferring Quaternary sea-level changes

<p>Targeted analysis of organic matter in soils and sediments is useful for evaluating past environmental conditions, as specific compounds may be directly linked to organisms and hence to the conditions in which they inhabited the environment.  Variations in molecular fossil distributions have become a powerful tool for understanding changes in palaeoclimate conditions.  This work uses molecular fossils to give an insight into the impact of transgressive events on primary producers inhabiting the studied basin, and hence a more detailed record of sea-level change.</p><p>The cores studied consisted of unconsolidated immature sediments from the mid-late Pleistocene (< 500,000 years) and the Holocene.  Molecular fossils, such as chlorophyll pigments and lipids, exhibit fluctuations as a response to changes in palaeoenvironmental conditions, providing a useful marker for sea-level changes.  Fluctuations in the pigment and <em>n</em>-alkane distribution reflect changes in primary producer activity, while the GDGT-based index of branched and isoprenoid tetraether lipids (BIT) differentiates between terrigenous and marine organic matter inputs.  Lipids were analysed by GC-FID and HPLC-MS while analysis of chlorophyll pigments was carried out using a new UHPLC-DAD method.</p><p>The results from biomarker analyses show excellent time-resolved agreement with previous lithological and ecological studies, but enabled a more sensitive response of different primary producers to changing conditions to be observed.  The molecular fossils were able to detect the onset and cessation of the studied transgressions earlier than it was possible with microfossil evidence.  Linking the pigment and lipid record with more secure dating will enable a more accurate record of Quaternary relative sea-level change.</p>

Molecular fossils reveal ancient associations of dsDNA viruses with several phyla of fungi

Little is known about the infections of double-stranded DNA (dsDNA) viruses in fungi. Here, we use a paleovirological method to systematically identify the footprints of past dsDNA virus infections within the fungal genomes. We uncover two distinct groups of endogenous nucleocytoplasmic large DNA viruses (NCLDVs) in at least seven fungal phyla (accounting for about a third of known fungal phyla), revealing an unprecedented diversity of dsDNA viruses in fungi. Interestingly, one fungal dsDNA virus lineage infecting six fungal phyla is closely related to the giant virus Pithovirus, suggesting giant virus relatives might widely infect fungi. Co-speciation analyses indicate fungal NCLDVs mainly evolved through cross-species transmission. Taken together, our findings provide novel insights into the diversity and evolution of NCLDVs in fungi.