Deep learning of genomic variation and regulatory network data

The human genome is now investigated through high throughput functional assays, and through the generation of population genomic data. These advances support the identification of functional genetic variants and the prediction of traits (eg. deleterious variants and disease). This review summarizes lessons learned from the large-scale analyses of genome and exome datasets, modeling of population data and machine learning strategies to solve complex genomic sequence regions. The review also portrays the rapid adoption of artificial intelligence/deep neural networks in genomics; in particular, deep learning approaches are well suited to model the complex dependencies in the regulatory landscape of the genome, and to provide predictors for genetic variant calling and interpretation

Early Cretaceous to present latitude of the central proto-Tibetan Plateau: A paleomagnetic synthesis with implications for Cenozoic tectonics, paleogeography, and climate of Asia

International audienc

Inclination shallowing in the Eocene Linzizong sediments from Tibet: correction, possible causes and implications for reconstructing the India-Asia collision

A systematic bias towards low palaeomagnetic inclination recorded in clastic sediments, that is, inclination shallowing, has been recognized and studied for decades. Identification, understanding and correction of this inclination shallowing are critical for palaeogeographic reconstructions, particularly those used in climatemodels and to date collisional events in convergent orogenic systems, such as those surrounding the Neotethys. Here we report palaeomagnetic inclinations from the sedimentary Eocene upper Linzizong Group of Southern Tibet that are ∼20◦ lower than conformable underlying volcanic units. At face value, the palaeomagnetic results from these sedimentary rocks suggest the southern margin of Asia was located ∼10◦N, which is inconsistent with recent reviews of the palaeolatitude of Southern Tibet. We apply two different correction methods to estimate the magnitude of inclination shallowing independently from the volcanics. The mean inclination is corrected from 20.5◦ to 40.0◦ within 95 per cent confidence limits between 33.1◦ and 49.5◦ by the elongation/inclination (E/I) correction method; an anisotropy-based inclination correction method steepens the mean inclination to 41.3 ± 3.3◦ after a curve fitting- determined particle anisotropy of 1.39 is applied. These corrected inclinations are statistically indistinguishable from the well-determined 40.3 ± 4.5o mean inclination of the underlying volcanic rocks that provides an independent check on the validity of these correction methods. Our results show that inclination shallowing in sedimentary rocks can be corrected. Careful inspection of stratigraphic variations of rock magnetic properties and remanence anisotropy suggests shallowing was caused mainly by a combination of syn- and post-depositional processes such as particle imbrication and sedimentary compaction that vary in importance throughout the section. Palaeolatitudes calculated from palaeomagnetic directions from Eocene sedimentary rocks of the upper Linzizong Group that have corrected for inclination shallowing are consistent with palaeolatitude history of the Lhasa terrane, and suggest that the India–Asia collision began at ∼20◦N by 45–55 Ma

Restoration of Cenozoic deformation in Asia and the size of Greater India

A long‐standing problem in the geological evolution of the India‐Asia collision zone is how and where convergence between India and Asia was accommodated since collision. Proposed collision ages vary from 65 to 35 Ma, although most data sets are consistent with collision being underway by 50 Ma. Plate reconstructions show that since 50 Ma ∼2400–3200 km (west to east) of India‐Asia convergence occurred, much more than the 450–900 km of documented Himalayan shortening. Current models therefore suggest that most post‐50 Ma convergence was accommodated north of the Indus‐Yarlung suture zone. We review kinematic data and construct an updated restoration of Cenozoic Asian deformation to test this assumption. We show that geologic studies have documented 600–750 km of N‐S Cenozoic shortening across, and north of, the Tibetan Plateau. The Pamir‐Hindu Kush region accommodated ∼1050 km of N‐S convergence. Geological evidence from Tibet is inconsistent with models that propose 750–1250 km of eastward extrusion of Indochina. Approximately 250 km of Indochinese extrusion from 30 to 20 Ma of Indochina suggested by SE Asia reconstructions can be reconciled by dextral transpression in eastern Tibet. We use our reconstruction to calculate the required size of Greater India as a function of collision age. Even with a 35 Ma collision age, the size of Greater India is 2–3 times larger than Himalayan shortening. For a 50 Ma collision, the size of Greater India from west to east is ∼1350–2600 km, consistent with robust paleomagnetic data from upper Cretaceous‐Paleocene Tethyan Himalayan strata. These estimates for the size of Greater India far exceed documented shortening in the Himalaya. We conclude that most of Greater India was consumed by subduction or underthrusting, without leaving a geological record that has been recognized at the surface

Greater India Basin hypothesis and a two-stage Cenozoic collision between India and Asia

Cenozoic convergence between the Indian and Asian plates produced the archetypical continental collision zone comprising the Himalaya mountain belt and the Tibetan Plateau. How and where India–Asia convergence was accommodated after collision at or before 52 Ma remains a long-standing controversy. Since 52 Ma, the two plates have converged up to 3,600 ± 35 km, yet the upper crustal shortening documented from the geological record of Asia and the Himalaya is up to approximately 2,350-km less. Here we show that the discrepancy between the convergence and the shortening can be explained by subduction of highly extended continental and oceanic Indian lithosphere within the Himalaya between approximately 50 and 25 Ma. Paleomagnetic data show that this extended continental and oceanic “Greater India” promontory resulted from 2,675 ± 700 km of North–South extension between 120 and 70 Ma, accommodated between the Tibetan Himalaya and cratonic India. We suggest that the approximately 50 Ma “India”–Asia collision was a collision of a Tibetan-Himalayan microcontinent with Asia, followed by subduction of the largely oceanic Greater India Basin along a subduction zone at the location of the Greater Himalaya. The “hard” India–Asia collision with thicker and contiguous Indian continental lithosphere occurred around 25–20 Ma. This hard collision is coincident with far-field deformation in central Asia and rapid exhumation of Greater Himalaya crystalline rocks, and may be linked to intensification of the Asian monsoon system. This two-stage collision between India and Asia is also reflected in the deep mantle remnants of subduction imaged with seismic tomography

Reply to Aitchison and Ali: Reconciling Himalayan ophiolite and Asian magmatic arc records with a two-stage India-Asia collision model

International audienc

Data report: revised composite depth scale and splice for IODP Site U1406

Integrated Ocean Drilling Program (IODP) Expedition 342 recovered exceptional Paleogene to early Neogene sedimentary archives from clay-rich sediments in the northwest Atlantic Ocean. These archives present an opportunity to study Cenozoic climate in a highly sensitive region at often unprecedented resolution. Such studies require continuous records in the depth and time domains. Using records from multiple adjacent drilled holes, intervals within consecutive cores are typically spliced into a single composite record on board the R/V JOIDES Resolution using high-resolution physical properties data sets acquired before the cores are split. The highly dynamic nature of the sediment drifts drilled during Expedition 342 and the modest amplitude of variance in the physical property records made it possible to construct only highly tentative initial working splices, which require extensive postexpedition follow-up work. Postexpedition, high-resolution X-ray fluorescence (XRF) core scanning data enabled the construction of a preliminary composite depth scale and splice. Here, we present the revised composite depth scale and splice for IODP Site U1406, predominantly constructed using detailed hole-to-hole correlations of newly generated high-resolution XRF data and revisions of the initial XRF data set. The revised composite depth scale and splice serve as a reference framework for future research on Site U1406 sediments