9 Works

Data from: Markov-modulated continuous-time Markov chains to identify site- and branch-specific evolutionary variation in BEAST

Guy Baele, Mandev Gill, Paul Bastide, Philippe Lemey & Marc Suchard
Markov models of character substitution on phylogenies form the foundation of phylogenetic inference frameworks. Early models made the simplifying assumption that the substitution process is homogeneous over time and across sites in the molecular sequence alignment. While standard practice adopts extensions that accommodate heterogeneity of substitution rates across sites, heterogeneity in the process over time in a site-specific manner remains frequently overlooked. This is problematic, as evolutionary processes that act at the molecular level are...

Data from: A search for technosignatures from TRAPPIST-1, LHS 1140, and 10 planetary systems in the Kepler field with the Green Bank Telescope at 1.15–1.73 GHz

Jean-Luc Margot, Pavlo Pinchuk, Adam H. Greenberg, Thomas Ayalde, Chad Bloxham, Arjun Boddu, Luis Gerardo Chinchilla-Garcia, Micah Cliffe, Sara Gallagher, Kira Hart, Brayden Hesford, Inbal Mizrahi, Ruth Pike, Dominic Rodger, Bade Sayki, Una Schneck, Aysen Tan, & Ryan S. Lynch
This dataset includes candidate signal detections obtained at the Green Bank Telescope in 2017 and reprocessed with the 2020 UCLA SETI Group data processing pipeline. As part of our ongoing search for technosignatures, we collected over three terabytes of data in May 2017 with the L-band receiver (1.15–1.73 GHz) of the 100 m diameter Green Bank Telescope. These observations focused primarily on planetary systems in the Kepler field, but also included scans of the recently...

Data from: Understanding past population dynamics: Bayesian coalescent-based modeling with covariates

Mandev S. Gill, Philippe Lemey, Shannon N. Bennett, Roman Biek & Marc A. Suchard
Effective population size characterizes the genetic variability in a population and is a parameter of paramount importance in population genetics and evolutionary biology. Kingman's coalescent process enables inference of past population dynamics directly from molecular sequence data, and researchers have developed a number of flexible coalescent-based models for Bayesian nonparametric estimation of the effective population size as a function of time. Major goals of demographic reconstruction include identifying driving factors of effective population size, and...

Computed tomography reveals hip dysplasia in the extinct Pleistocene saber-tooth cat Smilodon

Mairin Balisi, Abhinav Sharma, Carrie Howard, Christopher Shaw, Robert Klapper & Emily Lindsey
Reconstructing the behavior of extinct species is challenging, particularly for those with no living analogues. However, damage preserved as paleopathologies on bone can record how an animal moved in life, potentially reflecting behavioral patterns. Here, we assess hypothesized etiologies of pathology in a pelvis and associated right femur of a Smilodon fatalis saber-toothed cat, one of the best-studied species from the Pleistocene-age Rancho La Brea asphalt seeps, California, USA, using visualization by computed tomography (CT)....

Data from: A quantitative electrophysiological biomarker of duplication 15q11.2-q13.1 syndrome

Joel Frohlich, Damla Senturk, Vidya Saravanapandian, Peyman Golshani, Lawrence T. Reiter, Raman Sankar, Ronald Thibert, Charlotte Distefano, Scott Huberty, Edwin H. Cook & Shafali S. Jeste
Background: Duplications of 15q11.2-q13.1 (Dup15q syndrome) are highly penetrant for autism spectrum disorder (ASD). A distinct electrophysiological (EEG) pattern characterized by excessive activity in the beta band has been noted in clinical reports. We asked whether EEG power in the beta band, as well as in other frequency bands, distinguished children with Dup15q syndrome from those with non-syndromic ASD and then examined the clinical correlates of this electrophysiological biomarker in Dup15q syndrome. Methods: In the...

Sex-dimorphic effects of Biogenesis of Lysosome-related Organelles Complex-1 (BLOC-1) deficiency on mouse perinatal brain development

Cristina Ghiani & Esteban Dell'Angelica
The function(s) of the Biogenesis of Lysosome-related Organelles Complex 1 (BLOC-1) during brain development is hitherto largely unknown. Here, we investigated how its absence alters the trajectory of postnatal brain development using as model the pallid mouse. Most of the defects observed early postnatally in the mutant mice were more prominent in males than in females and in the hippocampus. Male mutant mice, but not females, had smaller brains as compared to sex-matching wild-types at...

Data from: Inferring heterogeneous evolutionary processes through time: from sequence substitution to phylogeography

Filip Bielejec, Philippe Lemey, Guy Baele, Andrew Rambaut & Marc A. Suchard
Molecular phylogenetic and phylogeographic reconstructions generally assume time-homogeneous substitution processes. Motivated by computational convenience, this assumption sacrifices biological realism and offers little opportunity to uncover the temporal dynamics in evolutionary histories. Here, we propose an evolutionary approach that explicitly relaxes the time-homogeneity assumption by allowing the specification of different infinitesimal substitution rate matrices across different time intervals, called epochs, along the evolutionary history. We focus on an epoch model implementation in a Bayesian inference framework...

Data from: The early spread and epidemic ignition of HIV-1 in human populations

Nuno R. Faria, Andrew Rambaut, Marc A. Suchard, Guy Baele, Trevor Bedford, Melissa J. Ward, Andrew J. Tatem, João D. Sousa, Nimalan Arinaminpathy, Jacques Pépin, David Posada, Martine Peeters, Oliver P. Pybus & Philippe Lemey
Thirty years after the discovery of HIV-1, the early transmission, dissemination and establishment of the virus in human populations remain unclear. Using statistical approaches applied to HIV-1 sequence data from central Africa, we show that from the 1920s Kinshasa was the focus of early transmission and the source of pre-1960 pandemic viruses elsewhere. Location and dating estimates were validated using the earliest HIV-1 archival sample, also from Kinshasa. The epidemic histories of HIV-1 group M...

Data from: Thyroid hormone protects primary cortical neurons exposed to hypoxia by reducing DNA methylation and apoptosis

Jianrong Li, Kiyomi Abe, Anna Milanesi, Yan-Yun Liu & Gregory A. Brent
Traumatic Brain Injury (TBI) is associated with disruption of cerebral blood flow leading to localized brain hypoxia. Thyroid hormone (TH) treatment, administered shortly after injury, has been shown to promote neural protection in rodent TBI models. The mechanism of TH protection, however, is not established. We used mouse primary cortical neurons to investigate the effectiveness and possible pathways of T3-promoted cell survival after exposure to hypoxic injury. Cultured primary cortical neurons were exposed to hypoxia...

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Affiliations

  • David Geffen School of Medicine at UCLA
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  • University of California Los Angeles
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  • KU Leuven
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