Bio

Education & Certifications


  • Master of Science, Stanford University, BIOM-MS (2015)
  • Bachelor of Science, Massachusetts Institute of Technology, Biology (2011)

Publications

All Publications


  • Inference of gorilla demographic and selective history from whole-genome sequence data. Molecular biology and evolution McManus, K. F., Kelley, J. L., Song, S., Veeramah, K. R., Woerner, A. E., Stevison, L. S., Ryder, O. A., Ape Genome Project, G., Kidd, J. M., Wall, J. D., Bustamante, C. D., Hammer, M. F. 2015; 32 (3): 600-612

    Abstract

    Although population-level genomic sequence data have been gathered extensively for humans, similar data from our closest living relatives are just beginning to emerge. Examination of genomic variation within great apes offers many opportunities to increase our understanding of the forces that have differentially shaped the evolutionary history of hominid taxa. Here, we expand upon the work of the Great Ape Genome Project by analyzing medium to high coverage whole-genome sequences from 14 western lowland gorillas (Gorilla gorilla gorilla), 2 eastern lowland gorillas (G. beringei graueri), and a single Cross River individual (G. gorilla diehli). We infer that the ancestors of western and eastern lowland gorillas diverged from a common ancestor approximately 261 ka, and that the ancestors of the Cross River population diverged from the western lowland gorilla lineage approximately 68 ka. Using a diffusion approximation approach to model the genome-wide site frequency spectrum, we infer a history of western lowland gorillas that includes an ancestral population expansion of 1.4-fold around 970 ka and a recent 5.6-fold contraction in population size 23 ka. The latter may correspond to a major reduction in African equatorial forests around the Last Glacial Maximum. We also analyze patterns of variation among western lowland gorillas to identify several genomic regions with strong signatures of recent selective sweeps. We find that processes related to taste, pancreatic and saliva secretion, sodium ion transmembrane transport, and cardiac muscle function are overrepresented in genomic regions predicted to have experienced recent positive selection.

    View details for DOI 10.1093/molbev/msu394

    View details for PubMedID 25534031

  • popRange: a highly flexible spatially and temporally explicit Wright-Fisher simulator. Source code for biology and medicine McManus, K. F. 2015; 10: 6-?

    Abstract

    Sequencing and genotyping technology advancements have led to massive, growing repositories of spatially explicit genetic data and increasing quantities of temporal data (i.e., ancient DNA). These data will allow more complex and fine-scale inferences about population history than ever before; however, new methods are needed to test complex hypotheses.This article presents popRange, a forward genetic simulator, which incorporates large-scale genetic data with stochastic spatially and temporally explicit demographic and selective models. Features such as spatially and temporally variable selection coefficients and demography are incorporated in a highly flexible manner. popRange is implemented as an R package and presented with an example simulation exploring a selected allele's trajectory in multiple subpopulations.popRange allows researchers to evaluate and test complex scenarios by simulating large-scale data with complicated demographic and selective features. popRange is available for download at http://cran.r-project.org/web/packages/popRange/index.html.

    View details for DOI 10.1186/s13029-015-0036-4

    View details for PubMedID 25883677

  • A Novel Test for Selection on cis-Regulatory Elements Reveals Positive and Negative Selection Acting on Mammalian Transcriptional Enhancers MOLECULAR BIOLOGY AND EVOLUTION Smith, J. D., McManus, K. F., Fraser, H. B. 2013; 30 (11): 2509-2518

    Abstract

    Measuring natural selection on genomic elements involved in the cis-regulation of gene expression-such as transcriptional enhancers and promoters-is critical for understanding the evolution of genomes, yet it remains a major challenge. Many studies have attempted to detect positive or negative selection in these noncoding elements by searching for those with the fastest or slowest rates of evolution, but this can be problematic. Here, we introduce a new approach to this issue, and demonstrate its utility on three mammalian transcriptional enhancers. Using results from saturation mutagenesis studies of these enhancers, we classified all possible point mutations as upregulating, downregulating, or silent, and determined which of these mutations have occurred on each branch of a phylogeny. Applying a framework analogous to Ka/Ks in protein-coding genes, we measured the strength of selection on upregulating and downregulating mutations, in specific branches as well as entire phylogenies. We discovered distinct modes of selection acting on different enhancers: although all three have experienced negative selection against downregulating mutations, the selection pressures on upregulating mutations vary. In one case, we detected positive selection for upregulation, whereas the other two had no detectable selection on upregulating mutations. Our methodology is applicable to the growing number of saturation mutagenesis data sets, and provides a detailed picture of the mode and strength of natural selection acting on cis-regulatory elements.

    View details for DOI 10.1093/molbev/mst134

    View details for Web of Science ID 000326745300011

    View details for PubMedID 23904330

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