9 Works

Data from: Purifying selection maintains dosage-sensitive genes during degeneration of the threespine stickleback Y chromosome

Michael A. White, Jun Kitano & Catherine L. Peichel
Sex chromosomes are subject to unique evolutionary forces that cause suppression of recombination, leading to sequence degeneration and the formation of heteromorphic chromosome pairs (i.e., XY or ZW). Although progress has been made in characterizing the outcomes of these evolutionary processes on vertebrate sex chromosomes, it is still unclear how recombination suppression and sequence divergence typically occur and how gene dosage imbalances are resolved in the heterogametic sex. The threespine stickleback fish (Gasterosteus aculeatus) is...

Data from: The impacts of Wolbachia and the microbiome on mate choice in Drosophila melanogaster

Devin Arbuthnott, Tera C. Levin & Daniel E. L. Promislow
Symbionts and parasites can manipulate their hosts’ reproduction to their own benefit, profoundly influencing patterns of mate choice and evolution of the host population. Wolbachia is one of the most widespread symbionts among arthropods, and one that alters its hosts’ reproduction in diverse and dramatic ways. While we are beginning to appreciate how Wolbachia's extreme manipulations of host reproduction can influence species diversification and reproductive isolation, we understand little about how symbionts and Wolbachia, in...

Data from: Cell signaling-based classifier predicts response to induction therapy in elderly patients with acute myeloid leukemia

Alessandra Cesano, Cheryl L. Willman, Kenneth J. Kopecky, Urte Gayko, Santosh Putta, Brent Louie, Matt Westfall, Norman Purvis, David C. Spellmeyer, Carol Marimpietri, Aileen C. Cohen, James Hackett, Jing Shi, Michael G. Walker, Zhuoxin Sun, Elisabeth Paietta, Martin S. Tallman, Larry D. Cripe, Susan Atwater, Frederick R. Appelbaum & Jerald P. Radich
Single-cell network profiling (SCNP) data generated from multi-parametric flow cytometry analysis of bone marrow (BM) and peripheral blood (PB) samples collected from patients >55 years old with non-M3 AML were used to train and validate a diagnostic classifier (DXSCNP) for predicting response to standard induction chemotherapy (complete response [CR] or CR with incomplete hematologic recovery [CRi] versus resistant disease [RD]). SCNP-evaluable patients from four SWOG AML trials were randomized between Training (N = 74 patients...

Data from: Quantifying MCMC exploration of phylogenetic tree space

Chris Whidden, & Frederick A. Matsen
In order to gain an understanding of the effectiveness of phylogenetic Markov chain Monte Carlo (MCMC), it is important to understand how quickly the empirical distribution of the MCMC converges to the posterior distribution. In this paper we investigate this problem on phylogenetic tree topologies with a metric that is especially well suited to the task: the subtree prune-and-regraft (SPR) metric. This metric directly corresponds to the minimum number of MCMC rearrangements required to move...

Data from: Annotation of pseudogenic gene segments by massively parallel sequencing of rearranged lymphocyte receptor loci

Jared Dean, Ryan O. Emerson, Marissa Vignali, Anna M. Sherwood, Mark J. Rieder, Christopher S. Carlson & Harlan Robins
Background: The adaptive immune system generates a remarkable range of antigen-specific T-cell receptors (TCRs), allowing the recognition of a diverse set of antigens. Most of this diversity is encoded in the complementarity determining region 3 (CDR3) of the β chain of the αβ TCR, which is generated by somatic recombination of noncontiguous variable (V), diversity (D), and joining (J) gene segments. Deletion and non-templated insertion of nucleotides at the D-J and V-DJ junctions further increases...

Data from: Does plasticity enhance or dampen phenotypic parallelism? A test with three lake-stream stickleback pairs.

Krista B. Oke, Mehvish Bukhari, Renaud Kaeuffer, Gregor Rolshausen, Katja Räsänen, Daniel I. Bolnick, Catherine L. Peichel & Andrew P. Hendry
Parallel (and convergent) phenotypic variation is most often studied in the wild, where it is difficult to disentangle genetic versus environmentally-induced effects. As a result, the potential contributions of phenotypic plasticity to parallelism (and non-parallelism) are rarely evaluated in a formal sense. Phenotypic parallelism could be enhanced by plasticity that causes stronger parallelism across populations in the wild than would be expected from genetic differences alone. Phenotypic parallelism could be dampened if site-specific plasticity induced...

Data from: Global circulation patterns of seasonal influenza viruses vary with antigenic drift

Trevor Bedford, Steven Riley, Ian G. Barr, Shobha Broor, Mandeep Chadha, Nancy J. Cox, Rodney S. Daniels, C. Palani Gunasekaran, Aeron C. Hurt, Anne Kelso, Alexander Klimov, Nicola S. Lewis, Xiyan Li, John W. McCauley, Takato Odagiri, Varsha Potdar, Andrew Rambaut, Yuelong Shu, Eugene Skepner, Derek J. Smith, Marc A. Suchard, Masato Tashiro, Dayan Wang, Xiyan Xu, Philippe Lemey … & Colin A. Russell
Understanding the spatiotemporal patterns of emergence and circulation of new human seasonal influenza virus variants is a key scientific and public health challenge. The global circulation patterns of influenza A/H3N2 viruses are well characterized1, 2, 3, 4, 5, 6, 7, but the patterns of A/H1N1 and B viruses have remained largely unexplored. Here we show that the global circulation patterns of A/H1N1 (up to 2009), B/Victoria, and B/Yamagata viruses differ substantially from those of A/H3N2...

Data from: Differences in rheotactic responses contribute to divergent habitat use between parapatric lake and stream threespine stickleback

Yuexin Jiang, Louisa Torrance, Catherine L. Peichel & Daniel I. Bolnick
Migration among populations is widely thought to undermine adaptive divergence, assuming gene flow arises from random movement of individuals. If individuals instead differ in dispersal behavior, phenotype-dependent dispersal can reduce the effective rate of gene flow or even facilitae divergence. For example, parapatric populations of lake and stream stickleback tend to actively avoid dispersing into the adjoining habitat.. However, the behavioral basis of this non-random dispersal was previously unknown. Here we show that lake and...

Data from: Allogeneic HY antibodies detected 3 months after female-to-male HCT predict chronic GVHD and nonrelapse mortality in humans

Hideki Nakasone, Lu Tian, Bita Sahaf, Takakazu Kawase, Kelsi Schoenrock, Spenser Perloff, Christine E. Ryan, Jed Paul, Rakesh Popli, Fang Wu, Joanne M. Otani, John Coller, & David B. Miklos
Allogeneic antibodies against minor histocompatibility antigens encoded on the Y chromosome (HY-Abs) develop after hematopoietic cell transplant (HCT) of male recipients with female donors (F→M). However, the temporal association between HY-Ab development and chronic graft-versus-host disease (cGVHD) has yet to be elucidated. We studied 136 adult F→M HCT patients, with plasma prospectively collected through 3 years posttransplant, and measured immunoglobulin G against 6 H-Y antigens. Multiple HY-Abs were frequently detected beginning at 3 months posttransplant:...

Registration Year

  • 2015

Resource Types

  • Dataset


  • Fred Hutchinson Cancer Research Center
  • Stanford University
  • The University of Texas at Austin
  • National Institute of Infectious Diseases
  • The Bronx Defenders
  • University of Washington
  • Stanford University School of Medicine
  • University of Cambridge
  • Malankara Orthodox Syrian Church Medical College Hospital
  • Adaptive Biotechnologies (United States)