Jan van Dam
Utrecht University
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The Geologic Time Scale 2012 | 2012
F.J. Hilgen; Lucas J. Lourens; Jan van Dam
An Astronomically Tuned Neogene Time Scale (ATNTS2012) is presented, as an update of ATNTS2004 in GTS2004. The new scale is not fundamentally different from its predecessor and the numerical ages are identical or almost so. Astronomical tuning has in principle the potential of generating a stable Neogene time scale as a function of the accuracy of the La2004 astronomical solution used for both scales. Minor problems remain in the tuning of the Lower Miocene. In GTS2012 we will summarize what has been modified or added since the publication of ATNTS2004 for incorporation in its successor, ATNTS2012. Mammal biostratigraphy and its chronology are elaborated, and the regional Neogene stages of the Paratethys and New Zealand are briefy discussed. To keep changes to ATNTS2004 transparent we maintain its subdivision into headings as much as possible.
Nature | 2006
Jan van Dam; Hayfaa Abdul Aziz; M. Ángeles Álvarez Sierra; F.J. Hilgen; Lars W. van den Hoek Ostende; Lucas J. Lourens; Pierre Mein; Albert Jan van der Meulen; Pablo Peláez-Campomanes
Mammals are among the fastest-radiating groups, being characterized by a mean species lifespan of the order of 2.5 million years (Myr). The basis for this characteristic timescale of origination, extinction and turnover is not well understood. Various studies have invoked climate change to explain mammalian species turnover, but other studies have either challenged or only partly confirmed the climate–turnover hypothesis. Here we use an exceptionally long (24.5–2.5 Myr ago), dense, and well-dated terrestrial record of rodent lineages from central Spain, and show the existence of turnover cycles with periods of 2.4–2.5 and 1.0 Myr. We link these cycles to low-frequency modulations of Milankovitch oscillations, and show that pulses of turnover occur at minima of the 2.37-Myr eccentricity cycle and nodes of the 1.2-Myr obliquity cycle. Because obliquity nodes and eccentricity minima are associated with ice sheet expansion and cooling and affect regional precipitation, we infer that long-period astronomical climate forcing is a major determinant of species turnover in small mammals and probably other groups as well.
Palaeogeography, Palaeoclimatology, Palaeoecology | 1999
Jan van Dam; Gert Jan Weltje
Abstract End-member modelling is applied to a data set of relative abundances of 67 Upper Miocene rodent associations (11–6 Ma) from Spain, France, Austria and Greece. The analysis results in the robust estimation of relative levels of four climatic parameters: humidity, temperature, seasonality type and predictability. In the preparatory stage, species are aggregated into nine groups on the basis of ecological criteria. Humidity preferences and adaptations are based on actualistic and functional morphological interpretations of dentition and locomotion. Temperature preferences are inferred from palaeobiogeographic distributions. Levels of adaptation to seasonality type (wet–dry or cool–warm seasonality) are assigned on the basis of diversities in present-day climate/vegetation zones, and the ability of extant relatives to hibernate. Demographic data are used to formulate adaptations to climatic (un)predictability. In the modelling stage, the compositions are unmixed into the contributions of four end members. These four extreme, theoretical rodent compositions are interpreted in climatic terms, and their contributions to the samples are used for the estimation of climatic parameters. The subset of 44 well-dated rodent compositions from the Calatayud-Daroca and Teruel basins (NE Spain) is used to construct detailed climatic curves for the Late Miocene, while the geographical dimension in the data set is used to calculate inter-basinal differences. The model results for Spain indicate more humid and cooler conditions between 10.5 and 8.5 Ma, around 7, and around 6 Ma, and more arid and warmer conditions before 10.5, between 8.6 and 7.5 Ma and around 6.5 Ma. Superimposed on this pattern is a shift from a more predictable, cool–warm seasonal climate towards a more unpredictable, wet–dry seasonal climate between 9.4 and 8.2 Ma. Inter-basinal comparisons per time slice show that the climate in southern Europe was dryer, warmer, more wet–dry seasonal and more unpredictable than in central Europe, and that the climatic and vegetational boundaries between the two regions were sharp. The occurrences of more humid and cooler episodes in Spain during the Late Miocene might be explained by southward migrations of the boundary between a temperate and subtropical-dry climatic belt and their associated vegetation types. Various positive correlations are observed between the rodent-based climatic curves for Spain, and other palaeoclimatic records from the Mediterranean and NE Atlantic region (clay minerals, marine fauna, stable isotopes). The two cooling maxima at 9.4 and 7 Ma closely correspond to clusters of marine events which are generally considered to reflect maxima of global ice volume.
Applied and Environmental Microbiology | 2006
Liang Wu; Jan van Dam; Dick Schipper; M.T.A. Penia Kresnowati; Angela M. Proell; Cor Ras; Wouter A. van Winden; Walter M. van Gulik; Joseph J. Heijnen
ABSTRACT The in vivo kinetics in Saccharomyces cerevisiae CEN.PK 113-7D was evaluated during a 300-second transient period after applying a glucose pulse to an aerobic, carbon-limited chemostat culture. We quantified the responses of extracellular metabolites, intracellular intermediates in primary metabolism, intracellular free amino acids, and in vivo rates of O2 uptake and CO2 evolution. With these measurements, dynamic carbon, electron, and ATP balances were set up to identify major carbon, electron, and energy sinks during the postpulse period. There were three distinct metabolic phases during this time. In phase I (0 to 50 seconds after the pulse), the carbon/electron balances closed up to 85%. The accumulation of glycolytic and storage compounds accounted for 60% of the consumed glucose, caused an energy depletion, and may have led to a temporary decrease in the anabolic flux. In phase II (50 to 150 seconds), the fermentative metabolism gradually became the most important carbon/electron sink. In phase III (150 to 300 seconds), 29% of the carbon uptake was not identified in the measurements, and the ATP balance had a large surplus. These results indicate an increase in the anabolic flux, which is consistent with macroscopic balances of extracellular fluxes and the observed increase in CO2 evolution associated with nonfermentative metabolism. The identified metabolic processes involving major carbon, electron, and energy sinks must be taken into account in in vivo kinetic models based on short-term dynamic metabolome responses.
Journal of Chromatography A | 2008
Reza M. Seifar; Zheng Zhao; Jan van Dam; Wouter A. van Winden; Walter M. van Gulik; Joseph J. Heijnen
A rapid, sensitive and selective ion-pair reversed-phase liquid chromatography-electrospray ionization isotope dilution tandem mass spectrometry (IP-LC-ESI-ID-MS/MS) was developed for quantitative analysis of free intracellular metabolites in cell cultures. As an application a group of compounds involved in penicillin biosynthesis pathway of Penicillium chrysogenum cells, such as penicillin G (PenG), 6-aminopenicillanic acid (6-APA), benzylpenicilloic acid (PIO), ortho-hydroxyphenyl acetic acid (o-OH-PAA), phenylacetic acid (PAA), 6-oxopipeidine-2-carboxylic acid (OPC), 8-hydroxypenicillic acid (8-HPA), L-alpha-(delta-aminoadipyl)-L-alpha-cystenyl-D-alpha-valine (ACV) and isopenicillin N (IPN) were chosen. (13)C-labeled analogs of the metabolites were added to the sample solutions as internal standards (I.S.). Sample mixtures were analyzed without any sample pretreatment. No extraction recovery check was needed because I.S. was added to the cell samples before extraction process. The method showed excellent precision (relative standard deviation (RSD)<or=11%, except for PIO and 8-HPA) in present of interferences from sample matrix. Limits of quantification (LOQs) for all metabolites were below 1 microM level.
International Journal for Parasitology | 2012
Jurgen R. Haanstra; Arjen van Tuijl; Jan van Dam; Wouter A. van Winden; Aloysius G.M. Tielens; Jaap J. van Hellemond; Barbara M. Bakker
Our quantitative knowledge of carbon fluxes in the long slender bloodstream form (BSF) Trypanosoma brucei is mainly based on non-proliferating parasites, isolated from laboratory animals and kept in buffers. In this paper we present a carbon balance for exponentially growing bloodstream form trypanosomes. The cells grew with a doubling time of 5.3h, contained 46 μ mol of carbon (10(8) cells)(-1) and had a glucose consumption flux of 160 nmol min(-1) (10(8) cells)(-1). The molar ratio of pyruvate excreted versus glucose consumed was 2.1. Furthermore, analysis of the (13)C label distribution in pyruvate in (13)C-glucose incubations of exponentially growing trypanosomes showed that glucose was the sole substrate for pyruvate production. We conclude that the glucose metabolised in glycolysis was hardly, if at all, used for biosynthetic processes. Carbon flux through glycolysis in exponentially growing trypanosomes was 10 times higher than the incorporation of carbon into biomass. This biosynthetic carbon is derived from other precursors present in the nutrient rich growth medium. Furthermore, we found that the glycolytic flux was unaltered when the culture went into stationary phase, suggesting that most of the ATP produced in glycolysis is used for processes other than growth.
Palaeogeography, Palaeoclimatology, Palaeoecology | 2002
Sabrina Renaud; Jan van Dam
Abstract Dental size and shape evolution in a Late Miocene lineage of murine rodents is analyzed, based on a set of deposits from the Teruel Basin (Spain). The lineage leads from Progonomys hispanicus, characterized by small and primitive molars, to Stephanomys ramblensis, characterized by large and specialized, stephanodont molars. A dietary change from granivory to herbivory is assumed to accompany this morphological change. Fourier analysis of molar outlines shows that size and shape evolve gradually with time. However, evolutionary rates of size and shape of upper and lower molars differ along the lineage. This suggests that mosaic evolution occurs with respect to upper and lower molars, and that size and shape are under different selective pressures. Comparison with biotic factors, i.e. diversity of the local community, and abiotic parameters, i.e. climatic reconstruction based on the rodent community and marine δ18O record, suggests that morphological evolution may be influenced by environmental variations. Climatic changes are suggested to influence biotic variations via opening of new ecological niches, favoring morphological evolution in murine rodents during the Late Miocene.
PLOS ONE | 2013
Isaac Casanovas-Vilar; Jan van Dam
Both functional adaptation and phylogeny shape the morphology of taxa within clades. Herein we explore these two factors in an integrated way by analyzing shape and size variation in the mandible of extant squirrels using landmark-based geometric morphometrics in combination with a comparative phylogenetic analysis. Dietary specialization and locomotion were found to be reliable predictors of mandible shape, with the prediction by locomotion probably reflecting the underlying diet. In addition a weak but significant allometric effect could be demonstrated. Our results found a strong phylogenetic signal in the family as a whole as well as in the main clades, which is in agreement with the general notion of squirrels being a conservative group. This fact does not preclude functional explanations for mandible shape, but rather indicates that ancient adaptations kept a prominent role, with most genera having diverged little from their ancestral clade morphologies. Nevertheless, certain groups have evolved conspicuous adaptations that allow them to specialize on unique dietary resources. Such adaptations mostly occurred in the Callosciurinae and probably reflect their radiation into the numerous ecological niches of the tropical and subtropical forests of Southeastern Asia. Our dietary reconstruction for the oldest known fossil squirrels (Eocene, 36 million years ago) show a specialization on nuts and seeds, implying that the development from protrogomorphous to sciuromorphous skulls was not necessarily related to a change in diet.
Journal of Human Evolution | 2011
Isaac Casanovas-Vilar; Jan van Dam; Salvador Moyà-Solà; Lorenzo Rook
Oreopithecus bambolii is one of the few hominoids that evolved under insular conditions, resulting in the development of unique adaptations that have fueled an intensive debate. The palaeoenvironment associated with this great ape has been the subject of great controversy as well. On the one hand, palaeobotanical data indicate that Oreopithecus likely inhabited mixed mesophytic forests interrupted by swamps; on the other hand, an abundance of hypsodont bovids points towards the existence of dry and open environments. Here, we provide a new approach based on the ecomorphology of the extinct endemic Muridae (rats and mice) of the so-called Oreopithecus faunas. Our results show that the successive species of endemic insular murids (Huerzelerimys and Anthracomys) evolved a number of adaptations observed only in extant family members that include significant proportions of grass in their diet. While this fits the pattern exhibited by large mammals, it contrasts with the available palaeobotanical information, which indicates that grasses were minor components of the vegetation. This contradiction may be explained because these endemic murids may have been adapted to the consumption of particular food items such as hard parts of aquatic plants (as shown by some extant murid species). However, because it is unlikely that the remaining herbivore mammals were adapted to this diet as well, we favour an alternative hypothesis that takes into account the peculiar ecological conditions of insular ecosystems leading to a density-dependent selective regime with strong competition. Such a regime would promote the selection of dental adaptations to increase feeding efficiency and durability of the dentition (such as hypsodonty) as seen in some fossil insular ruminants. This hypothesis requires further testing, but may partly account for parallel evolution of dental traits in phylogenetically unrelated insular mammals.
Archive | 1996
Jan van Dam
Landmark based morphometric methods were used to study shape variation in fossil murid teeth. Nineteen landmarks were defined and recorded on the occlusal surfaces of first upper molars belonging to eight populations from Late Miocene and Pliocene localities in Spain. The study focused on an evolutionary sequence characterized by development towards a specialized crown structure known as stephanodonty. Population differences were investigated using Bookstein shape coordinates and analyzed using analysis of variance and Mahalanobis distances. Relative warp analysis was used to study the nature of the shape variation among the landmarks. The results are consistent with the accepted taxonomic classification, although the taxonomic position of one of the populations is problematic. The analyses show that the development towards stephanodonty (a feature defined by the presence of ridges) is correlated with changes in shape, which are themselves correlated with size in the evolutionary sequence studied. It is apparent that landmark-based approaches show promise for functional morphological and paleoenvironmental interpretations of fossil murid teeth.