Publications by authors named "Nathan K Schaefer"

The disproportionate expansion of telencephalic structures during human evolution involved tradeoffs that imposed greater connectivity and metabolic demands on midbrain dopaminergic neurons. Despite the central role of dopaminergic neurons in human-enriched disorders, molecular specializations associated with human-specific features and vulnerabilities of the dopaminergic system remain unexplored. Here, we establish a phylogeny-in-a-dish approach to examine gene regulatory evolution by differentiating pools of human, chimpanzee, orangutan, and macaque pluripotent stem cells into ventral midbrain organoids capable of forming long-range projections, spontaneous activity, and dopamine release.

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Deletion of functional sequence is predicted to represent a fundamental mechanism of molecular evolution. Comparative genetic studies of primates have identified thousands of human-specific deletions (hDels), and the -regulatory potential of short (≤31 base pairs) hDels has been assessed using reporter assays. However, how structural variant-sized (≥50 base pairs) hDels influence molecular and cellular processes in their native genomic contexts remains unexplored.

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Comparative studies of great apes provide a window into our evolutionary past, but the extent and identity of cellular differences that emerged during hominin evolution remain largely unexplored. We established a comparative loss-of-function approach to evaluate whether human cells exhibit distinct genetic dependencies. By performing genome-wide CRISPR interference screens in human and chimpanzee pluripotent stem cells, we identified 75 genes with species-specific effects on cellular proliferation.

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Comparative studies of great apes provide a window into our evolutionary past, but the extent and identity of cellular differences that emerged during hominin evolution remain largely unexplored. We established a comparative loss-of-function approach to evaluate whether changes in human cells alter requirements for essential genes. By performing genome-wide CRISPR interference screens in human and chimpanzee pluripotent stem cells, we identified 75 genes with species-specific effects on cellular proliferation.

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Cell fusions have a long history of supporting biomedical research. These experimental models, historically referred to as 'somatic cell hybrids', involve combining the plasma membranes of two cells and merging their nuclei within a single cytoplasm. Cell fusion studies involving human and chimpanzee pluripotent stem cells, rather than somatic cells, highlight the need for responsible communication and a revised nomenclature.

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Many humans carry genes from Neanderthals, a legacy of past admixture. Existing methods detect this archaic hominin ancestry within human genomes using patterns of linkage disequilibrium or direct comparison to Neanderthal genomes. Each of these methods is limited in sensitivity and scalability.

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Article Synopsis
  • The protein-coding gene neuro-oncological ventral antigen 1 (NOVA1) is crucial for brain development and differs between modern humans and our extinct relatives, the Neanderthals and Denisovans.
  • Researchers used genome editing to introduce an ancient version of this gene into modern human cells and studied its effects on brain organoids.
  • The archaic version of NOVA1 slowed neural development and changed the complexity and electrical properties of the organoids, suggesting that human-specific changes to this gene may have influenced our evolution.
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Biological and chemical DNA fragmentation generates DNA molecules with a variety of termini, including blunt ends and single-stranded overhangs. We have developed a Next Generation Sequencing (NGS) assay, XACTLY, to interrogate the termini of fragmented DNA, information traditionally lost in standard NGS library preparation methods. Here we describe the XACTLY method, showcase its sensitivity and specificity, and demonstrate its utility in in vitro experiments.

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Article Synopsis
  • The passenger pigeon, once the most numerous bird in North America, had surprisingly low genetic diversity despite its large population size.
  • Genetic analysis involving mitochondrial and nuclear genomes revealed that rapid adaptive evolution may have led to the loss of neutral genetic diversity.
  • These findings challenge previous theories linking population instability to the passenger pigeon's quick extinction, highlighting the significant impact of natural selection on its genome.
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Background: Inferring the ancestry of each region of admixed individuals' genomes is useful in studies ranging from disease gene mapping to speciation genetics. Current methods require high-coverage genotype data and phased reference panels, and are therefore inappropriate for many data sets. We present a software application, AD-LIBS, that uses a hidden Markov model to infer ancestry across hybrid genomes without requiring variant calling or phasing.

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It is well established that related species hybridize and that this can have varied but significant effects on speciation and environmental adaptation. It should therefore come as no surprise that hybridization is not limited to species that are alive today. In the last several decades, advances in technologies for recovering and sequencing DNA from fossil remains have enabled the assembly of high-coverage genome sequences for a growing diversity of organisms, including many that are extinct.

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