Ancient DNA complements microfossil record in deep-sea subsurface sediments

Deep-sea subsurface sediments are the most important archives of marine biodiversity. Until now, these archives were studied mainly using the microfossil record, disregarding large amounts of DNA accumulated on the deep-sea floor. Accessing ancient DNA (aDNA) molecules preserved down-core would offer unique insights into the history of marine biodiversity, including both fossilized and non-fossilized taxa. Here, we recover aDNA of eukaryotic origin across four cores collected at abyssal depths in the South Atlantic, in up to 32.5 thousand-year-old sediment layers. Our study focuses on Foraminifera and Radiolaria, two major groups of marine microfossils also comprising diverse non-fossilized taxa. We describe their assemblages in down-core sediment layers applying both micropalaeontological and environmental DNA sequencing approaches. Short fragments of the foraminiferal and radiolarian small subunit rRNA gene recovered from sedimentary DNA extracts provide evidence that eukaryotic aDNA is preserved in deep-sea sediments encompassing the last glacial maximum. Most aDNA were assigned to non-fossilized taxa that also dominate in molecular studies of modern environments. Our study reveals the potential of aDNA to better document the evolution of past marine ecosystems and opens new horizons for the development of deep-sea palaeogenomics.     

Diversity and geographic distribution of benthic foraminifera: a molecular perspective

The diversity and distribution of modern benthic foraminifera has been extensively studied in order to aid the paleoecological interpretation of their fossil record. Traditionally, foraminiferal species are identified based on morphological characters of their organic, agglutinated or calcareous tests. Recently, however, new molecular techniques based on analysis of DNA sequences have been introduced to study the genetic variation in foraminifera. Although the number of species for which DNA sequence data exist is still very limited, it appears that morphology-based studies largely underestimated foraminiferal diversity. Here, we present two examples of the use of DNA sequences to examine the diversity of benthic foraminifera. The first case deals with molecular and morphological variations in the well-known and common calcareous genus Ammonia. The second case presents molecular diversity in the poorly documented group of monothalamous (single-chambered) foraminifera. Both examples perfectly illustrate high cryptic diversity revealed in almost all molecular studies. Molecular results also confirm that the majority of foraminiferal species have a restricted geographic distribution and that globally distributed species are rare. This is in opposition to the theory that biogeography has no impact on the diversity of small-sized eukaryotes. At least in the case of foraminifera, size does not seem to have a main impact on dispersal capacities. However, the factors responsible for the dispersal of foraminiferal species and the extension of their geographic ranges remain largely unknown. Special Issue: Protist diversity and geographic distribution. Guest editor: W. Foissner.     

Palaeoenvironmental conditions preceding the Messinian Salinity Crisis: A case study from Gavdos Island

The Messinian pre-evaporitic sedimentary succession of Gavdos Island (Metochia section) is a nearly uninterrupted succession of marine sediments, dominated by finely laminated diatomaceous marls, which are cyclically alternating with clayey diatomites and white diatomites. The qualitative and quantitative analysis of the planktonic foraminiferal fauna allowed the recognition of nine bioevents, which have been astronomically dated for the Mediterranean. The base of the diatomitic succession in Gavdos Island is dated at 6.722 Ma and the top at 6.015 Ma. The studied section contains benthic foraminiferal genera characteristic of an outer shelf to slope environment. The qualitative and quantitative analysis of this microfauna revealed three benthic foraminiferal fossil assemblages and the occurrence of allochthonous species transported into the bathyal environment by current activity. The cyclical pattern of the benthic foraminifera assemblages indicates that the studied sediments have been affected by repeated episodes of basin restriction characterized by low diversity benthic foraminifera populations, and a limited planktonic foraminifer association typified by shallow, surface-dwelling forms. This restriction was partly due to Antarctic cooling, which produced palaeo-Mediterranean sea-level oscillations during the Early Messinian, as a prelude to closure of the Atlantic connections. The relative impact of climatic versus tectonic control on sedimentation patterns within this basin is discussed.     

Sensitivity of south‐east Atlantic planktonic foraminifera to mid‐Pleistocene climate change

Abstract: The last one million years are important in terms of climate development during the so‐called Mid‐Pleistocene Transition when amplification of the glacial–interglacial cycles occurred. This study describes abundance changes in fossil planktonic foraminifera in sediments from Core T89‐40, retrieved from the Walvis Ridge in the south‐east Atlantic, across this time period. Cycles between upwelling and subtropical planktonic foraminiferal assemblages are shown to mirror changes between glacial and interglacial periods, respectively. During interglacial marine isotopic stages (MIS) 9, 11 and 31, however, anomalously high abundances of the polar left‐coiled Neogloboquadrina pachyderma occur, presumably linked to unusual seasonal upwelling waters. The planktonic foraminiferal abundance record shows 41‐ky cyclic variations in the regional oceanography linked to cycles in insolation influenced by changes in the Earth’s axial tilt (obliquity). These orbitally induced oscillations in oceanographic change occurred throughout the entire record. The most conspicuous feature of the planktonic foraminiferal record is the near absence of left‐coiled Globorotalia truncatulinoides between 960 and 610 ka (MIS 26‐15). The abrupt disappearance of this species is synchronous with the onset of the Mid‐Pleistocene Transition in MIS 26.     

Late Holocene deep-sea benthic foraminifera from the Sea of Marmara

The benthic foraminiferal assemblages of two cores from the late-Holocene, organic-carbon-rich and carbonate-poor, deep-sea sediments of the eastern depression of the Sea of Marmara have been studied. They were deposited under high level of primary productivity and poorly oxygenated bottom-water conditions; they show low diversity and are dominated by a group of species adapted to an infaunal life style with wide bathymetric distribution (ca. 70–2000 m) in the Mediterranean Sea. Oxygen deficiency down to about 0.5 ml/l does not seem adversely to affect the rate of reproduction of the dominant species belonging to Melonis, Chilostomella, buliminids, and bolivinitids. Their distribution is primarily controlled by substrate conditions.Faunal similarities with fossil assemblages in association with some late-Quaternary sapropels and related facies from the eastern Mediterranean basins suggest that they were deposited under palaeo-oceanographic conditions closely similar to those of the modern Sea of Marmara.     

Modern foraminiferal record of alternating open and restricted environmental conditions in the Santo André lagoon,SW Portugal

Benthic foraminifera from eleven stations sampled seasonally were analyzed in order to examine the biological response to rapid and intense environmental changes taking place in the Santo André coastal lagoon. Foraminiferal assemblages show a very low species diversity and a high dominance of three euryhaline species throughout the year. Under closed-inlet conditions, foraminiferal assemblages exhibit low abundance of foraminiferal tests, whereas under open-inlet conditions absolute abundance greatly increases due to sea water entrance. Present-day dramatic environmental changes are thought to be responsible for deformed foraminiferal tests that are commonly found. Comparison of modern assemblages with those obtained from the Holocene sedimentary record indicates persistent restrictive environmental conditions after sandy barrier formation, circa 5000 years ago.     

Multiscale climate change impacts on plant diversity in the Atacama Desert

Comprehending ecological dynamics requires not only knowledge of modern communities but also detailed reconstructions of ecosystem history. Ancient DNA (aDNA) metabarcoding allows biodiversity responses to major climatic change to be explored at different spatial and temporal scales. We extracted aDNA preserved in fossil rodent middens to reconstruct late Quaternary vegetation dynamics in the hyperarid Atacama Desert. By comparing our paleo‐informed millennial record with contemporary observations of interannual variations in diversity, we show local plant communities behave differentially at different timescales. In the interannual (years to decades) time frame, only annual herbaceous expand and contract their distributional ranges (emerging from persistent seed banks) in response to precipitation, whereas perennials distribution appears to be extraordinarily resilient. In contrast, at longer timescales (thousands of years) many perennial species were displaced up to 1,000 m downslope during pluvial events. Given ongoing and future natural and anthropogenically induced climate change, our results not only provide baselines for vegetation in the Atacama Desert, but also help to inform how these and other high mountain plant communities may respond to fluctuations of climate in the future.     

An optimized method for the extraction of ancient eukaryote DNA from marine sediments

Marine sedimentary ancient DNA (sedaDNA) provides a powerful means to reconstruct marine palaeo‐communities across the food web. However, currently there are few optimized sedaDNA extraction protocols available to maximize the yield of small DNA fragments typical of ancient DNA (aDNA) across a broad diversity of eukaryotes. We compared seven combinations of sedaDNA extraction treatments and sequencing library preparations using marine sediments collected at a water depth of 104 m off Maria Island, Tasmania, in 2018. These seven methods contrasted frozen versus refrigerated sediment, bead‐beating induced cell lysis versus ethylenediaminetetraacetic acid (EDTA) incubation, DNA binding in silica spin columns versus in silica‐solution, diluted versus undiluted DNA in shotgun library preparations to test potential inhibition issues during amplification steps, and size‐selection of low molecular‐weight (LMW) DNA to increase the extraction efficiency of sedaDNA. Maximum efficiency was obtained from frozen sediments subjected to a combination of EDTA incubation and bead‐beating, DNA binding in silica‐solution, and undiluted DNA in shotgun libraries, across 45 marine eukaryotic taxa. We present an optimized extraction protocol integrating these steps, with an optional post‐library LMW size‐selection step to retain DNA fragments of ≤500 base pairs. We also describe a stringent bioinformatic filtering approach for metagenomic data and provide a comprehensive list of contaminants as a reference for future sedaDNA studies. The new extraction and data‐processing protocol should improve quantitative paleo‐monitoring of eukaryotes from marine sediments, as well as other studies relying on the detection of highly fragmented and degraded eukaryote DNA in sediments.     

Benthic foraminifera associated with a hydrocarbon seep in the Rockall Trough (NE Atlantic)

Recent benthic foraminiferal assemblages in surface sediments of the Rockall Trough (NE Atlantic) have been qualitatively and quantitatively studied in order to investigate the effects of hydrocarbon seepage on benthic foraminiferal populations. Species diversity and abundance data have been examined in samples of similar lithology collected from hydrocarbon seep and non-seep (control) areas at a water depth of about 1000 m. Three species groups with different environmental preferences can be recognized. Group 1 dominates seep samples, and includes species tolerant to hydrocarbon emission, especially Angulogerina bradyana. In contrast, the less tolerant Group 2 species are weakly represented at seeps but dominate control samples. Group 3 species occur in low frequencies in both seep and non-seep samples. Furthermore, the measurement of species diversity (Shannon-Wiener and Simpson indices) demonstrates a difference in foraminiferal occurrence and frequencies between the seep and non-seep sites. Thus, the benthic foraminiferal distribution pattern is guided by different sensitivities of the species to hydrocarbons, reduced bottom-water oxygen usually associated with seepage and/or to a relatively elevated organic matter content in the sediment.     

Genetic diversity loss in a biodiversity hotspot: ancient DNA quantifies genetic decline and former connectivity in a critically endangered marsupial

The extent of genetic diversity loss and former connectivity between fragmented populations are often unknown factors when studying endangered species. While genetic techniques are commonly applied in extant populations to assess temporal and spatial demographic changes, it is no substitute for directly measuring past diversity using ancient DNA (aDNA). We analysed both mitochondrial DNA (mtDNA) and nuclear microsatellite loci from 64 historical fossil and skin samples of the critically endangered Western Australian woylie (Bettongia penicillata ogilbyi), and compared them with 231 (n = 152 for mtDNA) modern samples. In modern woylie populations 15 mitochondrial control region (CR) haplotypes were identified. Interestingly, mtDNA CR data from only 29 historical samples demonstrated 15 previously unknown haplotypes and detected an extinct divergent clade. Through modelling, we estimated the loss of CR mtDNA diversity to be between 46% and 91% and estimated this to have occurred in the past 2000–4000 years in association with a dramatic population decline. In addition, we obtained near‐complete 11‐loci microsatellite profiles from 21 historical samples. In agreement with the mtDNA data, a number of ‘new’ microsatellite alleles was only detected in the historical populations despite extensive modern sampling, indicating a nuclear genetic diversity loss >20%. Calculations of genetic diversity (heterozygosity and allelic rarefaction) showed that these were significantly higher in the past and that there was a high degree of gene flow across the woylie's historical range. These findings have an immediate impact on how the extant populations are managed and we recommend the implementation of an assisted migration programme to prevent further loss of genetic diversity. Our study demonstrates the value of integrating aDNA data into current‐day conservation strategies.     

Comparison of contemporary and fossil diatom assemblages from the western Antarctic Peninsula shelf

During the past ten years, the Antarctic Peninsula has been identified as the most rapidly warming region of the Southern Hemisphere and it is important to place this warming in the context of the natural climate and oceanographic variability of the recent geological past. Many biological proxies, such as marine diatom assemblages, have been used to determine Southern Ocean palaeoceanographic conditions during the Late Quaternary, however, few investigations have attempted to link observations of modern floras with the fossil record. In this study we examine a suite of modern austral spring (December 2003) and summer (February 2002) surface water samples from along the western Antarctic Peninsula (WAP) continental shelf and compare these to core-top, surface sediment samples. Using detrended correspondence analysis (DCA) and principal component analysis (PCA) of diatom abundance data we investigate the relationship of contemporary diatom floras with the fossil record. This multivariate analysis reveals that our modern assemblages can be divided into three groups: summer southern WAP sites, summer northern WAP sites, and spring WAP sites. Sea surface temperature (SST) is an important environmental variable for explaining seasonal differences in diatom assemblages between spring and summer, but sea surface salinity (SSS) is more important for understanding temporally-equivalent regional variations in assemblage. Our summer diatom samples are more reminiscent of early season assemblages, reflecting the unusually late sea ice retreat from the region that year. When the modern assemblages are compared to the fossil record, it is clear that most of the important diatoms from the summer assemblage are not preserved into the sediments, and that the fossil record more closely reflects spring assemblages. This observation is important for any future attempts to quantitatively reconstruct palaeoceanographic conditions along the WAP during the Late Quaternary and highlights the need for many more such studies in order to address longer timescales, such as interannual variability, in the context of the fossil record.     

Does fuel type influence the amount of charcoal produced in wildfires? Implications for the fossil record

Charcoal occurrence is extensively used as a tool for understanding wildfires over geological timescales. Yet, the fossil charcoal literature to date rarely considers that fire alone is capable of creating a bias in the abundance and nature of charcoal it creates, before it even becomes incorporated into the fossil record. In this study we have used state‐of‐the‐art calorimetry to experimentally produce charcoal from 20 species that represent a range of surface fuels and growth habits, as a preliminary step towards assessing whether different fuel types (and plant organs) are equally likely to remain as charcoal post‐fire. We observe that charcoal production appears to be species specific, and is related to the intrinsic physical and chemical properties of a given fuel. Our observations therefore suggest that some taxa are likely to be overrepresented in fossil charcoal assemblages (i.e. needle‐shed conifers, tree ferns) and others poorly represented, or not preserved at all (i.e. broad shoot‐shed conifers, weedy angiosperms, shrub angiosperms, some ferns). Our study highlights the complexity of charcoal production in modern fuels and we consider what a bias in charcoal production may mean for our understanding of palaeowildfires.     

Past grazing habitats for Svalbard reindeer indicated by the pollen content of 3300‐year‐old faeces from Edgeøya,Svalbard

Sedentary populations, like the Svalbard reindeer, tend to select the most nutritious and easily available plants during the different seasons. It has been shown that plants selected during grazing season are reflected in the pollen content of modern faeces from Svalbard reindeer. In this study the pollen and spore content of fossil reindeer faeces and peat from Raddedalen, western Edgeøya, Svalbard, are presented. The pollen content of the fossil faeces is first compared to published pollen data from modern Svalbard reindeer faeces so as to determine which season they were deposited, and second the pollen in the fossil faeces are compared to the pollen content of the peat in which they were found. The lower part of the peat section is dated to 3435±105?cal?yr BP. The faeces are dominated by pollen from early flowering species such as Saxifraga oppositifolia‐type, S. nivalis‐type, Brassicaceae, and Pedicularis spp. thereby indicating that grazing and faeces deposition took place in spring and early summer. The peat and faeces have some similarities in their pollen and spore content, but different methods of deposition and concentration of pollen in faeces and peat result in different fossil assemblages. The results suggests that the climate of Raddedalen was warmer and moister than today, allowing peat to form in the past.     

Diversity and palaeoecology of a highly diverse Late Triassic marine biota from the Cassian Formation of north Italy

A sample of marine invertebrates from the Late Triassic Cassian Formation (north Italy) yielded one of the most diverse Early Mesozoic fossil assemblages ever reported (c. 170 species). The assemblage was found in basin clays, but was transported from nearby carbonate platforms as indicated by fragmentation, microbial encrustation and the presence of coated grains and ooids. Most of the specimens are small (< 1 cm) reflecting both, small adult sizes and size sorting during transport. Rarefaction analysis suggests that diversity of surface collection and bulk sampling is the same. However, rank abundance, species richness and taxonomic composition differ strongly according to sampling method. Low‐grade lithification of the sediments is the main reason that high diversity can be recognized, because it facilitates disaggregation and finding of small molluscs. Sample standardization shows that the studied assemblage is much more diverse than known Early Triassic assemblages. However, its diversity is similar to that of Anisian assemblages. This suggests that recovery from the end‐Permian mass‐extinction was quite advanced in the Middle Triassic and alpha‐diversity remained high until the Late Triassic. According to current models, Early Triassic and Anisian faunas match the niche overlap phase of recovery during which diversity is built up by increasing alpha‐diversity, whereas beta‐diversity rises slowly. Subsequently, habitat width of species contracts because of increasing competition, making beta‐diversity the principal drive of overall diversity increase. The diversity pattern of various Late Triassic Cassian associations meets the predictions for the transition from the niche overlap to the habitat contraction phase.: Triassic, Cassian Formation, palaeoecology, diversity, mollusc dominance.     

The effect of bioturbation by polychaetes (Opheliidae) on benthic foraminiferal assemblages and test preservation

Biological activity such as burrowing can alter benthic foraminiferal shell preservation and may also modify benthic foraminiferal assemblages by vertical mixing, inducing sediment homogenization. Here, we analyse benthic foraminiferal assemblages and taphonomy of upper Miocene marine deposits from Conil de la Frontera (Cádiz, south‐western Spain). The deposits consist of marls displaying a pervasive alternation of intensively bioturbated beds dominated by Macaronichnus segregatis traces (ichnofabric index 4–5) and non‐bioturbated beds. Benthic foraminiferal assemblages are dominated by Cibicidoides mundulus and Cibicides refulgens, indicating that the marls were deposited on an oligotrophic, well‐oxygenated upper slope. The impact of burrowing on the preservation of benthic foraminiferal tests was tested using Q‐mode cluster analysis, which found two well‐differentiated groups of samples, one including the non‐bioturbated beds and the other encompassing the bioturbated ones. Fragmentation and recrystallization account for the differentiation of these groups, both being higher in the bioturbated sediments. Aggressive chemical digestion by the Macaronichnus trace‐makers, assumed to be a polychaete worm of the family Opheliidae, etched the microfossil shells, making them more vulnerable to fragmentation. Intense bioturbation favoured the circulation of pore fluids, encouraging recrystallization. Pervasive burrowing resulted in significant vertical reworking of microfossils. As a consequence, benthic foraminiferal assemblages in the bioturbated beds were homogenized in the mixed layer; that is, the uppermost layer of the substrate totally burrowed. The alternation of bioturbated and non‐bioturbated beds reflects episodic transfer of food particles down slope from shallower parts of the shelf as well as from the continent due to storms under otherwise homogeneous oligotrophic marine conditions.     

The genetic diversity of planktic foraminifera and the global distribution of ribosomal RNA genotypes

Fossil planktic foraminifers in the ocean sediments play an unparalleled role in our understanding of the oceanographic environment in the past. An in depth knowledge of their diversity, ecology and biogeography in the modern ocean lies central to the interpretation of the fossil assemblages. In comparison with their benthic counterparts, planktic foraminifera have a very limited diversity of around fifty extant morphospecies. Their morphospecies diversity peaks in the sub-tropics and decreases steeply towards the poles. Traditional species concepts have partitioned morphological types into distinct species (morphospecies) based on test shape, but genetic studies show that individual morphospecies are actually complexes of several discrete genetic types (genotypes). Many of these genotypes have distinct ecologies and novel adaptations that are consistent with species-level classification, indicating that the true diversity of planktic foraminifers has been greatly underestimated. Although planktic foraminifera are clearly capable of long-distance dispersal, they may be constrained by both physical and ecological barriers that vary according to the evolutionary history and ecology of the individual genotypes within a morphospecies. These differences lead to diverse biogeographies. Here, we provide an overview of the genetic and biogeographic data available to date for the planktic foraminifera and present global biogeographies highlighting the distribution of genetic types in the eight planktic foraminiferal morphospecies for which detailed molecular evidence is available.     

The thermal history of human fossils and the likelihood of successful DNA amplification

Recent success in the amplification of ancient DNA (aDNA) from fossil humans has led to calls for further tests to be carried out on similar material. However, there has been little systematic research on the survival of DNA in the fossil record, even though the environment of the fossil is known to be of paramount importance for the survival of biomolecules over archaeological and geological timescales. A better understanding of aDNA survival would enable research to focus on material with greater chances of successful amplification, thus preventing the unnecessary loss of material and valuable researcher time. We argue that the thermal history of a fossil is a key parameter for the survival of biomolecules. The thermal history of a number of northwest European Neanderthal cave sites is reconstructed here and they are ranked in terms of the relative likelihood of aDNA survival at the sites, under the assumption that DNA depurination is the principal mechanism of degradation. The claims of aDNA amplification from material found at Lake Mungo, Australia, are also considered in the light of the thermal history of this site.     

Ostracods had colonized estuaries by the late Silurian

The fossil record of terrestrialization documents notable shifts in the environmental and physiological tolerances of many animal and plant groups. However, for certain significant components of modern freshwater and terrestrial environments, the transition out of marine settings remains largely unconstrained. Ostracod crustaceans occupy an exceptional range of modern aquatic environments and are invaluable palaeoenvironmental indicators in the fossil record. However, pre-Carboniferous records of supposed non-marine and marginal marine ostracods are sparse, and the timing of their marine to non-marine transition has proven elusive. Here, we reassess the early environmental history of ostracods in light of new assemblages from the late Silurian of Vietnam. Two, low diversity but distinct ostracod assemblages are associated with estuarine deposits. This occurrence is consistent with previous incidental reports of ostracods occupying marginal and brackish settings through the late Silurian and Devonian. Therefore, ostracods were pioneering the occupation of marginal marine and estuarine settings 60 Myr before the Carboniferous and they were a component of the early phase of transition from marine to non-marine environments.     

The fossil record of the sixth extinction

Comparing the magnitude of the current biodiversity crisis with those in the fossil record is difficult without an understanding of differential preservation. Integrating data from palaeontological databases with information on IUCN status, ecology and life history characteristics of contemporary mammals, we demonstrate that only a small and biased fraction of threatened species (< 9%) have a fossil record, compared with 20% of non‐threatened species. We find strong taphonomic biases related to body size and geographic range. Modern species with a fossil record tend to be large and widespread and were described in the 19^th century. The expected magnitude of the current extinction based only on species with a fossil record is about half of that of one based on all modern species; values for genera are similar. The record of ancient extinctions may be similarly biased, with many species having originated and gone extinct without leaving a tangible record.     

Extinction of South American sparassodontans (Metatheria): environmental fluctuations or complex ecological processes?

Sparassodontans are a diverse but now extinct group of metatherians that were apex predators in South America during most of the Cenozoic. Studying their decline has been controversial mainly due to the scarcity of the fossil record, and different methodological approaches have led to contradictory hypotheses. In an effort to explore questions about their extinction, we developed a novel multi‐model statistical approach to analyse all of the currently available data at a continental scale. Using multiple regression analysis and new advances in beta diversity analysis, we used all currently available fossil data at a continental scale to test four competing hypotheses to account for the decline of sparassodontans: competition with placental carnivorans, competition with avian phorusrhacids, non‐competitive ecological interactions, and environmental fluctuations. Our results show that the sparassodontan extinction was a gradual process with species disappearing throughout the Cenozoic. Multiple regression analysis supported non‐competitive ecological interactions as the best extinction model. Native South American ungulates, African migrants (caviomorph rodents and platyrrhine primates) and didelphimorphians were the groups with the highest statistical significance. Sparassodontan beta diversity increased between South American Land Mammal Ages after the Paleocene–Eocene boundary. Our results demonstrate that ecological modelling techniques illuminate aspects of extinction processes whilst mitigating the limitations of the fossil record. Our study suggests that non‐competitive ecological interactions could have been the main driver for sparassodontan extinction rather than, as commonly assumed, a result of competition and/or abiotic fluctuations.