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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 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 

The genome of an individual from an admixed population consists of segments originated from different ancestral populations. Most existing ancestry inference approaches focus on calling these segments for the extant individual. In this paper, we present a general ancestry inference approach for inferring recent ancestors from an extant genome. Given the genome of an individual from a recently admixed population, our method can estimate the proportions of the genomes of the recent ancestors of this individual that originated from some ancestral populations. The key step of our method is the inference of ancestors (called founders) right after the formation of an admixed population. The inferred founders can then be used to infer the ancestry of recent ancestors of an extant individual. Our method is implemented in a computer program called PedMix2. To the best of our knowledge, there is no existing method that can practically infer ancestors beyond grandparents from an extant individual’s genome. Results on both simulated and real data show that PedMix2 performs well in ancestry inference. 

Abstract The North American craton interior preserves a >1 Ga history of near surface processes that inform ongoing debates regarding timing and drivers of continental‐scale deformation and erosion associated with far‐field orogenesis. We tested various models of structural inversion on a major segment of the Midcontinent Rift along the Douglas Fault in northern Wisconsin, which accommodated ≳10 km of total vertical displacement. U‐Pb detrital zircon and vein calcite Δ₄₇/U‐Pb thermochronometry from the hanging wall constrain the majority of uplift (≳8.5 km) and deformation to 1052–1036 Ma during the Ottawan phase of the Grenvillian orogeny. Combined U‐Pb zircon dates, Δ₄₇/U‐Pb calcite thermochronometry, and field data that document syn‐ to early post‐depositional deformation in the footwall constrain a second stage of uplift (1–1.5 km) ca. 995–980 Ma during the Rigolet phase of the Grenvillian orogeny. A minor phase of Appalachian far‐field orogenesis is associated with minimal thrust reactivation. Our combined analyses identified the 995–980 Ma Bayfield Group as a Grenvillian foreland basin with an original thickness 0.5–2 km greater than currently preserved. By quantifying flexural loading and other subsidence mechanisms along the Douglas Fault, we identify dynamic subsidence as a mechanism that could be consistent with the development of late‐Grenvillian transcontinental fluvial systems. Minimal post‐Grenvillian erosion (0.5–2 km) in this part of the craton interior has preserved the Bayfield Group and equivalent successions, limiting the magnitude of regional erosion that can be attributed to Neoproterozoic glaciation.