(Supplementary Material 2) Landmark coordinates of the analyzed specimens with associated metadata

The use of planktonic foraminifera in paleoceanographic studies relies on the assumption that morphospecies represent biological species with ecological preferences that are stable through time and space. However, genetic surveys unveiled a considerable level of diversity in most morphospecies of planktonic foraminifera. This diversity is significant for paleoceanographic applications because cryptic species were shown to display distinct ecological preferences that could potentially help refine paleoceanographic proxies. Subtle morphological differences between cryptic species of planktonic foraminifera have been reported, but so far their applicability within paleoceanographic studies remains largely unexplored. Here we show how information on genetic diversity can be transferred to paleoceanography using Globorotalia inflata as a case study. The two cryptic species of G. inflata are separated by the Brazil-Malvinas Confluence (BMC), a major oceanographic feature in the South Atlantic. Based on this observation, we developed a morphological model of cryptic species detection in core top material. The application of the cryptic species detection model to Holocene samples implies latitudinal oscillations in the position of the confluence that are largely consistent with reconstructions obtained from stable isotope data. We show that the occurrence of cryptic species in G. inflata, can be detected in the fossil record and used to trace the migration of the BMC. Since a similar degree of morphological separation as in G. inflata has been reported from other species of planktonic foraminifera, the approach presented in this study can potentially yield a wealth of new paleoceanographical proxies.

Benthic foraminifera of the Red Sea

The distribution of living (Rose Bengal-stained), dead and fossil benthic foraminifera was investigated in six short cores (multicores, 30-32 cm total length) recovered from the central Red Sea. The ecological preferences as well as the relationship between the live and dead/fossil assemblages (preserved down-core) were examined. The sites, located along a W-E profile and between the depth of 366 and 1782 m, extend from the center of the oxygen minimum zone (OMZ, ~200-650 m), through its margin at ~600 m, and down to the well-aerated deep-water environment. Live (Rose-Bengal stained) and coexisting dead foraminifera were studied in the upper 5 cm of each of the sites, and the fossil record was studied down to ~32 cm. Q-mode Principal Component Analysis was used and four distinct foraminiferal fossil assemblages were determined. These assemblages follow different water mass properties. In the center of the OMZ, where the organic carbon content is highest and the oxygen concentration is lowest (<=0.5 ml O2/l), the Bolivina persiensis-Bulimina marginata-Discorbinella rhodiensis assemblage dominates. The slightly more aerated and lower organic-carbon-content seafloor, at the margin of the OMZ, is characterized by the Neouvigerina porrecta-Gyroidinoides cf. G. soldanii assemblage. The transitional environment, between 900-1200 m, with its well-aerated and oligotrophic seafloor, is dominated by the Neouvigerina ampullacea-Cibicides mabahethi assemblage. The deeper water (>1500 m), characterized by the most oxygenated and oligotrophic seafloor conditions, is associated with the Astrononion sp. A-Hanzawaia sp. A assemblage. Throughout the Red Sea extremely high values of temperature and salinity are constant below ~200 m depth, but the flux of organic matter to the sea floor varies considerably with bathymetry and appears to be the main controlling factor governing the distribution pattern of the benthic foraminifera. Comparison between live and the dead/fossil assemblages reveals a large difference between the two. Processes that may control this difference include species-specific high turnover rates, and preferential predation and loss of fragile taxa (either by chemical or microbial processes). Significant variations in the degree of loss of the organic-cemented agglutinants were observed down core. This group is preserved down to 5-10 cm at the shallow OMZ sites and down to greater depths at well-aerated and oligotrophic sites. The lower rate of disintegration of these forms, in the deeper locations of the Red Sea, may be related to low microbial activity. This results in the preservation of increasing numbers of organic-cemented shells down-core.

Fidelity bias in mollusk assemblages from coastal lagoons of Southern Brazil

The South America southern coast exhibits many outcrops with abundant shell beds, from the Pleistocene through the Recent. How much biological information is preserved within these shell beds? Or, what is the actual probability a living community has to leave a fossil record corresponding to these shell deposits? Although ecological and biogeographical aspects might had been pointed, considering these temporal scales, up to the moment there is no taphonomically-oriented studies available. Quantitative comparisons between living (LAs), death (DAs) and fossil assemblages (FAs) are important not only in strictly taphonomic studies, but have grown a leading tool for conservation paleobiology analysis. Comparing LAs, DAs and FAs from estuaries and lagoons in the Rio Grande do Sul Coastal Plain makes possible to quantitatively understand the nature and quantity of biological information preserved in fossil associations in Holocene lagoon facies. As already noted by several authors, spatial scale parts the analysis, but we detected that the FAs refl ects live ones, rather than dead ones, as previously not realized. The results herein obtained illustrates that species present in DA are not as good preserved in recent (Holocene) fossil record as originally thought. Strictly lagoon species are most prone to leave fossil record. The authors consider that the fi delity pattern here observed for estuarine mollusks to be driven by (i) high temporal and spatial variability in the LAs, (ii) spatial mixing in the DA and (iii) differential preservation of shells, due to long residence times in the taphonomically active zone.

(Table 1) Sample descriptions, carbon contents, and lipid yields across the K/T boundary at DSDP Hole 93-605 and at Stevns Klint, Denmark

This reconnaissance study was undertaken to determine whether the mass extinctions and faunal successions that mark the Cretaceous/Tertiary (K/T) boundary left a discernible molecular fossil record in the sediments of this period. Lipid signatures of sediments taken from above and below the K/T boundary were compared in core and outcrop samples taken from two locations: the U.S. east coast continental margin (western Atlantic Ocean, DSDP Site 605) and Stevns Klint, Denmark. Four calcareous sediments taken from above and below the K/T boundary in DSDP Hole 605, Section 605-66-1, revealed changing lipid signatures between above and below that are characterized by a large component of unresolved naphthenic hydrocarbons and a homologous series of n-alkanes ranging from Ci6 to C33. These lipid signatures are attributed to an influx of a terrestrial higher plant component and to bacterial reworking of the sediments under partially anoxic depositional and/or diagenetic conditions. The outcrop samples from Stevns Klint had extremely low concentrations of indigenous lipids. The fish clay at the K/T boundary contained traces of microbial hydrocarbons and fatty acids, whereas the carbonates above and below had only microbial fatty acids and additional terrestrial resin acids. The data from both sites indicate a perturbation in the deposition of lipid compound classes across the K/T boundary.

Coccosphere geometry measurements from culture experiments on the coccolithophore species Calcidiscus leptoporus, Calcidiscus quadriperforatus and Helicosphaera carteri

Coccolithophores are a key phytoplankton group that exhibit remarkable diversity in their biology, ecology, and calcitic exoskeletons (coccospheres). An understanding of the physiological processes that underpin coccosphere architecture is essential for maximizing the information that can be retrieved from their extensive fossil record. Using culturing experiments on four modern species from three long-lived families, we investigate how coccosphere architecture responds to population shifts from rapid (exponential) to slowed (stationary) growth phases as nutrients become depleted. These experiments reveal statistical differences in cell size and the number of coccoliths per cell between these two growth phases, specifically that cells in exponential-phase growth are typically smaller with fewer coccoliths, whereas cells experiencing growth-limiting nutrient depletion have larger coccosphere sizes and greater numbers of coccoliths per cell. Although the exact numbers are species-specific, these growth-phase shifts in coccosphere geometry are common to four different coccolithophore families (Calcidiscaceae, Coccolithaceae, Isochrysidaceae, Helicosphaeraceae), demonstrating that this is a core physiological response to nutrient depletion across a representative diversity of this phytoplankton group. Polarised light microscopy was used for all coccosphere geometry measurements.

Carbon and oxygen isotope ratios of Selinde River, southeastern Siberian platform

Carbon isotopic data from the Selinde section in the southeastern part of the Siberian platform area are correlated with the reference isotopic profile from the Lower Cambrian stratotype sections of the Lena Aldan region, but also show additional d13C excursions unrecognized there. The chemostratigraphic correlation suggests that the geological and fossil record of the lower Pestrotsvet Formation in the Selinde section has a deeper history than the stratotype region. This conclusion is important for both constraining the age of the earliest Cambrian marine transgression on the Siberian platform and providing a clearer understanding of the pace and order of early Cambrian geochemical and biological events.

The relationship between vegetation and modern pollen assemblages on Mount Paggeo (NE Greece)

In this study, we investigated the relationship between vegetation and modern-pollen rain along the elevational gradient of Mount Paggeo. We apply multivariate data analysis to assess the relationship between vegetation and modern-pollen rain and quantify the representativeness of forest zones. This study represents the first statistical analysis of pollen-vegetation relationship along an elevational gradient in Greece. Hence, this paper improves confidence in interpretation of palynological records from north-eastern Greece and may refine past climate reconstructions for a more accurate comparison of data and modelling. Numerical classification and ordination were performed on pollen data to assess differences among plant communities that beech (Fagus sylvatica) dominates or co-dominates. The results show a strong relationship between altitude, arboreal cover, human impact and variations in pollen and nonpollen palynomorph taxa percentages.

A timescale for diatom evolution based on four molecular markers: reassessment of ghost lineages and major steps defining diatom evolution.

ABSTRACT. – Phylogenies and molecular clocks of the diatoms have largely been inferred from SSU rDNA sequences. A new phylogeny of diatoms was estimated using four gene markers SSU and LSU rDNA rbcL and psbA (total 4352 bp) with 42 diatom species. The four gene trees analysed with a maximum likelihood (ML) and Baysian (BI) analysis recovered a monophyletic origin of the new diatom classes with high bootstrap support, which has been controversial with single gene markers using single outgroups and alignments that do not take secondary structure of the SSU gene into account. The divergence time of the classes were calculated from a ML tree in the MultliDiv Time program using a Bayesian estimation allowing for simultaneous constraints from the fossil record and varying rates of molecular evolution of different branches in the phylogenetic tree. These divergence times are generally in agreement with those proposed by other clocks using single genes with the exception that the pennates appear much earlier and suggest a longer Cretaceous fossil record that has yet to be sampled. Ghost lineages (i.e. the discrepancy between first appearance (FA) and molecular clock age of origin from an extant taxon) were revealed in the pennate lineage, whereas those ghost lineages in the centric lineages previously reported by others are reviewed and referred to earlier literature.

A timescale for diatom evolution based on four molecular markers: reassessment of ghost lineages and major steps defining diatom evolution.

ABSTRACT. – Phylogenies and molecular clocks of the diatoms have largely been inferred from SSU rDNA sequences. A new phylogeny of diatoms was estimated using four gene markers SSU and LSU rDNA rbcL and psbA (total 4352 bp) with 42 diatom species. The four gene trees analysed with a maximum likelihood (ML) and Baysian (BI) analysis recovered a monophyletic origin of the new diatom classes with high bootstrap support, which has been controversial with single gene markers using single outgroups and alignments that do not take secondary structure of the SSU gene into account. The divergence time of the classes were calculated from a ML tree in the MultliDiv Time program using a Bayesian estimation allowing for simultaneous constraints from the fossil record and varying rates of molecular evolution of different branches in the phylogenetic tree. These divergence times are generally in agreement with those proposed by other clocks using single genes with the exception that the pennates appear much earlier and suggest a longer Cretaceous fossil record that has yet to be sampled. Ghost lineages (i.e. the discrepancy between first appearance (FA) and molecular clock age of origin from an extant taxon) were revealed in the pennate lineage, whereas those ghost lineages in the centric lineages previously reported by others are reviewed and referred to earlier literature.

Haptophyta

Haptophyta are predominantly planktonic and phototrophic organisms that have their main distribution in marine environments worldwide. They are a major component of the microbial ecosystem, some form massive blooms and some are toxic. Haptophytes are significant players in the global carbonate cycle through photosynthesis and calcification. They are characterized by the haptonema, a third appendage used for attachment and food handling, two similar flagella, two golden-brown chloroplasts, and organic body scales that serve in species identification. Coccolithophores have calcified scales termed coccoliths. Phylogenetically Haptophyta form a well-defined group and are divided into two classes Pavlovophyceae and Coccolithophyceae (Prymnesiophyceae). Currently, about 330 species are described. Environmental DNA sequencing shows high haptophyte diversity in the marine pico- and nanoplankton, of which many likely represent novel species and lineages. Haptophyte diversity is believed to have peaked in the past and their presence is documented in the fossil record back to the Triassic, approximately 225 million years ago. Some biomolecules of haptophyte origin are extraordinarily resistant to decay and are thus used by geologists as sedimentary proxies of past climatic conditions.

Haptophyta

Haptophyta are predominantly planktonic and phototrophic organisms that have their main distribution in marine environments worldwide. They are a major component of the microbial ecosystem, some form massive blooms and some are toxic. Haptophytes are significant players in the global carbonate cycle through photosynthesis and calcification. They are characterized by the haptonema, a third appendage used for attachment and food handling, two similar flagella, two golden-brown chloroplasts, and organic body scales that serve in species identification. Coccolithophores have calcified scales termed coccoliths. Phylogenetically Haptophyta form a well-defined group and are divided into two classes Pavlovophyceae and Coccolithophyceae (Prymnesiophyceae). Currently, about 330 species are described. Environmental DNA sequencing shows high haptophyte diversity in the marine pico- and nanoplankton, of which many likely represent novel species and lineages. Haptophyte diversity is believed to have peaked in the past and their presence is documented in the fossil record back to the Triassic, approximately 225 million years ago. Some biomolecules of haptophyte origin are extraordinarily resistant to decay and are thus used by geologists as sedimentary proxies of past climatic conditions.

A new echinoderm Lagerstätten in Portugal : preliminary results

Congresso realizado em Mendoza, Argentina de 28 de setembro a 3 de outubro de 2014

Ecological responses of Western Palearctic avian species to late Quaternary climate oscillations

This PhD thesis explores the ecological responses of bird species to glacial-interglacial transitions during the late Quaternary in the Western Palearctic, using multiple approaches and at different scales, enhancing the importance of the bird fossil record and quantitative methods to elucidate biotic trends in relation to long-term climate changes. The taxonomic and taphonomic analyses of the avian fossil assemblages from four Italian Middle and Upper Pleistocene sedimentary successions (Grotta del Cavallo, Grotta di Fumane, Grotta di Castelcivita, and Grotta di Uluzzo C) allowed us to reconstruct local-scale patterns in birds’ response to climate changes. These bird assemblages are characterized by the presence of temperate species and by the occasional presence of cold-dwelling species during glacials, related to range shifts. These local patterns are supported by those identified at the continental scale. In this respect, I mapped the present-day and LGM climatic envelopes of species with different climatic requirements. The results show a substantial stability in the range of temperate species and pronounced changes in the range of cold-dwelling species, supported by their fossil records. Therefore, the responses to climate oscillations are highly related to the thermal niches of investigated species. I also clarified the dynamics of the presence of boreal and arctic bird species in Mediterranean Europe, due to southern range shifts, during the glacial phases. After a reassessment of the reliability of the existing fossil evidence, I show that this phenomenon is not as common as previously thought, with important implications for the paleoclimatic and paleoenvironmental significance of the targeted species. I have also been able to explore the potential of multivariate and rarefaction methods in the analyses of avian fossils from Grotta del Cavallo. These approaches helped to delineate the main drivers of taphonomic damages and the dynamics of species diversity in relation to climate-driven paleoenvironmental changes.

Relationship between phenotype and environment in marine calcifying organisms: exploring growth and shell properties of different mollusks species in past and modern scenario

Coastal ecosystems represent an inestimable source of biodiversity, being among the most productive areas on the planet. Despite the great ecological and economic value of those environments, many threats endanger the species living in this ecosystem, like the rapid warming and the sea acidification, among many other. Benthic calcifying organisms (e.g. mollusks, corals and echinoderms) in particular, are among the most exposed to those hazards. These organisms use calcium carbonate as a structural and protective material through the biomineralization process, biologically controlled by the organism, but nevertheless, strongly influenced by the environmental surroundings. Evaluating how a changing environment can influence the process of biomineralization is critical to understand how those species of great ecological and economic importance will face the ongoing climate change. This thesis investigates the mechanism of biomineralization in different mollusks’ species of the Adriatic Sea, providing detailed descriptions of shells skeletal, biometric and growth parameters. Applying a multidisciplinary and multi-scale research approach, the influence of external environmental factors on the process of shell formation has been investigated. To achieve this purpose analysis were conducted both on current populations and on fossil remain, which allows to investigate ecological responses to past climate transitions. Mollusks’ shells in fact are one of the best tools to understand climate change in the past, present and future, since they record the environmental conditions prevailed during their life, reflected on the geochemical properties, microstructure and growth of the shell. This approach allowed to overcome the time scale limit imposed by field and laboratory survey, and better understand species long term adaptive response to changing environment, a crucial issue to define proper conservation and management strategies. Furthermore, the investigation of fossil record of mollusks assemblages offered the opportunity to evaluate the long-term biotic response to anthropogenic stressors in the north Adriatic Sea.