ALBERT

Beschreibung: Regulatory DNA elements, short genomic segments that regulate gene expression, have been implicated in developmental disorders and human disease. Despite this clinical urgency, only a small fraction of the regulatory DNA repertoire has been confirmed through reporter gene assays. The overall success rate of functional validation of candidate regulatory elements is low. Moreover, the number and diversity of datasets from which putative regulatory elements can be identified is large and rapidly increasing. We generated a flexible and user-friendly tool to integrate the information from different types of genomic datasets, e.g. ATAC-seq, ChIP-seq, conservation, aiming to increase the ease and success rate of functional prediction. To this end, we developed the EMERGE program that merges all datasets that the user considers informative and uses a logistic regression framework, based on validated functional elements, to set optimal weights to these datasets. ROC curve analysis shows that a combination of datasets leads to improved prediction of tissue-specific enhancers in human, mouse and Drosophila genomes. Functional assays based on this prediction can be expected to have substantially higher success rates. The resulting integrated signal for prediction of functional elements can be plotted in a build-in genome browser or exported for further analysis.

Beschreibung: Rates of erosion over time provide a valuable tool for gauging tectonic and climatic drivers of landscape evolution. Here, we measure 10 Be archived in quartz sediment from the Fish Creek-Vallecito basin to resolve a time-series of catchment averaged erosion rates and to test the hypothesis that aridity and increased climate variation after ca. 3 Ma led to an increase in erosion rates in this semi-arid, ice-free setting. The Fish Creek-Vallecito basin, located east of the Peninsular Ranges in southern California, is an ideal setting to derive a Plio-Pleistocene paleo-erosion rate record. The basin has a rapid sediment accumulation rate, a detailed magnetostratigraphic age record, and its stratigraphy has been exposed through recent, rapid uplift and erosion. A well-defined source region of uniform lithology and low erosion rate provides a high, reproducible 10 Be signal. We find that paleo-erosion rates were remarkably consistent between 1 and 4 Ma, averaging 38 ± 24 m/Myr (2 σ ). Modern catchment averaged erosion rates are similar to the paleo-erosion rates. The uniformity of erosion over the past 4 Myr indicates the landscape was not significantly affected by late Pliocene global climate change, nor was it affected by a local long-term increase in aridity.

Beschreibung: For four decades, the inability of nonhuman primates to produce human speech sounds has been claimed to stem from limitations in their vocal tract anatomy, a conclusion based on plaster casts made from the vocal tract of a monkey cadaver. We used x-ray videos to quantify vocal tract dynamics in living macaques during vocalization, facial displays, and feeding. We demonstrate that the macaque vocal tract could easily produce an adequate range of speech sounds to support spoken language, showing that previous techniques based on postmortem samples drastically underestimated primate vocal capabilities. Our findings imply that the evolution of human speech capabilities required neural changes rather than modifications of vocal anatomy. Macaques have a speech-ready vocal tract but lack a speech-ready brain to control it.

Beschreibung: In the context of future climate change, understanding the nature and behaviour of ice sheets during warm intervals in Earth history is of fundamental importance. The late Pliocene warm period (also known as the PRISM interval: 3.264 to 3.025 million years before present) can serve as a potential analogue for projected future climates. Although Pliocene ice locations and extents are still poorly constrained, a significant contribution to sea-level rise should be expected from both the Greenland ice sheet and the West and East Antarctic ice sheets based on palaeo sea-level reconstructions. Here, we present results from simulations of the Antarctic ice sheet by means of an international Pliocene Ice Sheet Modeling Intercomparison Project (PLISMIP-ANT). For the experiments, ice-sheet models including the shallow ice and shelf approximations have been used to simulate the complete Antarctic domain (including grounded and floating ice). We compare the performance of six existing numerical ice-sheet models in simulating modern control and Pliocene ice sheets by a suite of five sensitivity experiments. We include an overview of the different ice-sheet models used and how specific model configurations influence the resulting Pliocene Antarctic ice sheet. The six ice-sheet models simulate a comparable present-day ice sheet, considering the models are set up with their own parameter settings. For the Pliocene, the results demonstrate the difficulty of all six models used here to simulate a significant retreat or re-advance of the East Antarctic ice grounding line, which is thought to have happened during the Pliocene for the Wilkes and Aurora basins. The specific sea-level contribution of the Antarctic ice sheet at this point cannot be conclusively determined, whereas improved grounding line physics could be essential for a correct representation of the migration of the grounding-line of the Antarctic ice sheet during the Pliocene.

Beschreibung: The understanding of the nature and behavior of ice sheets in past warm periods is important for constraining the potential impacts of future climate change. The Pliocene warm period (between 3.264 and 3.025 Ma) saw global temperatures similar to those projected for future climates; nevertheless, Pliocene ice locations and extents are still poorly constrained. We present results from the efforts to simulate mid-Pliocene Greenland Ice Sheets by means of the international Pliocene Ice Sheet Modeling Intercomparison Project (PLISMIP). We compare the performance of existing numerical ice sheet models in simulating modern control and mid-Pliocene ice sheets with a suite of sensitivity experiments guided by available proxy records. We quantify equilibrated ice sheet volume on Greenland, identifying a potential range in sea level contributions from warm Pliocene scenarios. A series of statistical measures are performed to quantify the confidence of simulations with focus on inter-model and inter-scenario differences. We find that Pliocene Greenland Ice Sheets are less sensitive to differences in ice sheet model configurations and internal physical quantities than to changes in imposed climate forcing. We conclude that Pliocene ice was most likely to be limited to the highest elevations in eastern and southern Greenland as simulated with the highest confidence and by synthesizing available regional proxies; however, the extent of those ice caps needs to be further constrained by using a range of general circulation model (GCM) climate forcings.

Beschreibung: It is still an open question how equilibrium warming in response to increasing radiative forcing – the specific equilibrium climate sensitivity S – depends on background climate. We here present palaeodata-based evidence on the state dependency of S, by using CO2 proxy data together with a 3-D ice-sheet-model-based reconstruction of land ice albedo over the last 5 million years (Myr). We find that the land ice albedo forcing depends non-linearly on the background climate, while any non-linearity of CO2 radiative forcing depends on the CO2 data set used. This non-linearity has not, so far, been accounted for in similar approaches due to previously more simplistic approximations, in which land ice albedo radiative forcing was a linear function of sea level change. The latitudinal dependency of ice-sheet area changes is important for the non-linearity between land ice albedo and sea level. In our set-up, in which the radiative forcing of CO2 and of the land ice albedo (LI) is combined, we find a state dependence in the calculated specific equilibrium climate sensitivity, S[CO2,LI], for most of the Pleistocene (last 2.1 Myr). During Pleistocene intermediate glaciated climates and interglacial periods, S[CO2,LI] is on average ~ 45 % larger than during Pleistocene full glacial conditions. In the Pliocene part of our analysis (2.6–5 Myr BP) the CO2 data uncertainties prevent a well-supported calculation for S[CO2,LI], but our analysis suggests that during times without a large land ice area in the Northern Hemisphere (e.g. before 2.82 Myr BP), the specific equilibrium climate sensitivity, S[CO2,LI], was smaller than during interglacials of the Pleistocene. We thus find support for a previously proposed state change in the climate system with the widespread appearance of northern hemispheric ice sheets. This study points for the first time to a so far overlooked non-linearity in the land ice albedo radiative forcing, which is important for similar palaeodata-based approaches to calculate climate sensitivity. However, the implications of this study for a suggested warming under CO2 doubling are not yet entirely clear since the details of necessary corrections for other slow feedbacks are not fully known and the uncertainties that exist in the ice-sheet simulations and global temperature reconstructions are large.

Beschreibung: A still open question is how equilibrium warming in response to increasing radiative forcing – the specific equilibrium climate sensitivity S – is depending on background climate. We here present paleo-data based evidence on the state-dependency of S, by using CO2 proxy data together with 3-D ice-sheet model-based reconstruction of land ice albedo over the last 5 million years (Myr). We find that the land-ice albedo forcing depends non-linearly on the background climate, while any non-linearity of CO2 radiative forcing depends on the CO2 data set used. This non-linearity was in similar approaches not accounted for due to previously more simplistic approximations of land-ice albedo radiative forcing being a linear function of sea level change. Important for the non-linearity between land-ice albedo and sea level is a latitudinal dependency in ice sheet area changes.In our setup, in which the radiative forcing of CO2 and of the land-ice albedo (LI) is combined, we find a state-dependency in the calculated specific equilibrium climate sensitivity S[CO2,LI] for most of the Pleistocene (last 2.1 Myr). During Pleistocene intermediate glaciated climates and interglacial periods S[CO2,LI] is on average ∼ 45 % larger than during Pleistocene full glacial conditions. In the Pliocene part of our analysis (2.6–5 Myr BP) the CO2 data uncertainties prevents a well-supported calculation for S[CO2,LI], but our analysis suggests that during times without a large land-ice area in the Northern Hemisphere (e.g. before 2.82 Myr BP) the specific equilibrium climate sensitivity S[CO2,LI] was smaller than during interglacials of the Pleistocene. We thus find support for a previously proposed state-change in the climate system with the wide appearance of northern hemispheric ice sheets. This study points for the first time to a so far overlooked non-linearity in the land-ice albedo radiative forcing, which is important for similar paleo data-based approaches to calculate climate sensitivity. However, the implications of this study for a suggested warming under CO2 doubling are not yet entirely clear since the necessary corrections for other slow feedbacks are in detail unknown and the still existing uncertainties in the ice sheet simulations and global temperature reconstructions are large.