Search for: All records

In a multicellular organism, cell lineages share a common evolutionary history. Knowing this history can facilitate the study of development, aging, and cancer. Cell lineage trees represent the evolutionary history of cells sampled from an organism. Recent developments in single-cell sequencing have greatly facilitated the inference of cell lineage trees. However, single-cell data are sparse and noisy, and the size of single-cell data is increasing rapidly. Accurate inference of cell lineage tree from large single-cell data is computationally challenging. In this paper, we present ScisTree2, a fast and accurate cell lineage tree inference and genotype calling approach based on the infinite-sites model. ScisTree2 relies on an efficient local search approach to find optimal trees. ScisTree2 also calls single-cell genotypes based on the inferred cell lineage tree. Experiments on simulated and real biological data show that ScisTree2 achieves better overall accuracy while being significantly more efficient than existing methods. To the best of our knowledge, ScisTree2 is the first model-based cell lineage tree inference and genotype calling approach that is capable of handling datasets from tens of thousands of cells or more. 

Abstract The closure of the Mozambique Ocean defines the final assembly of the megacontinent Gondwana and is associated with a vast region of crustal growth in the Arabian-Nubian Shield. Despite this central paleogeographic position, there are few constraints on the position of terranes within and bounding the Mozambique Ocean. We report paleomagnetic data from ca. 726 Ma dikes exposed in southern Oman. Well-resolved magnetite magnetization is constrained to be primary by a conglomerate test on mafic clasts within overlying Cryogenian diamictite. The resulting paleomagnetic pole indicates that Oman was at a paleolatitude of 37 ± 2.5°N and was rotated ~80° counterclockwise from its present-day orientation. This position is consistent with Oman forming a contiguous plate with the India and South China cratons on the northern margin of the Mozambique Ocean in a distinct tectonic domain from Arabian-Nubian arcs to the south. This position reveals an ~5500-km-wide oceanic realm prior to subsequent closure that resulted in a major zone of Neoproterozoic crustal growth. 

Abstract Serpentine minerals have received a lot of attention because of their unique crystal structures, their wide occurrence in orogenic belts and their potential role in contributing seismic anisotropy in subducting slabs. Several studies have investigated crystal preferred orientation (CPO) in high temperature antigorite serpentinites from Japan, the Alps, Spain, Cuba and Tibet, documenting significant crystal alignment. However, only a limited number of lower grade serpentines have been explored to date. Mainly because of submicroscopic microstructural heterogeneities CPO cannot be measured with conventional methods such as optical microscopy and EBSD. In this study 15 serpentinites from different tectonic settings in California, the Central Alps and Northern Spain have been investigated, mainly with high energy synchrotron X-ray diffraction, to quantify bulk crystal alignment. We find that CPO is strong on sheared surfaces of fractured blocks and secondary veins but the bulk of most serpentinite samples, except high-grade recrystallized antigorite serpentinite, show only weak crystal alignment. Correspondingly calculated seismic anisotropy based on CPO is not very significant. This is supported by very heterogeneous microstructures as documented with SEM and TEM analyses. 

2024 SWLLIP manuscript release for submission 

Publication release of code, data, figures, and manuscript