36 Works

Data from: Seasonality in the migration and establishment of H3N2 Influenza lineages with epidemic growth and decline

Daniel Zinder, Trevor Bedford, Edward B. Baskerville, Robert J. Woods, Manojit Roy & Mercedes Pascual
Background: Influenza A/H3N2 has been circulating in humans since 1968, causing considerable morbidity and mortality. Although H3N2 incidence is highly seasonal, how such seasonality contributes to global phylogeographic migration dynamics has not yet been established. In this study, we incorporate time-varying migration rates in a Bayesian MCMC framework. We focus on migration within China and between China and North-America as case studies, then expand the analysis to global communities. Results: Incorporating seasonally varying migration rates...

Data from: A public database of memory and naive B-cell receptor sequences

William S. DeWitt, Paul Lindau, Thomas M. Snyder, Anna M. Sherwood, Marissa Vignali, Christopher S. Carlson, Philip D. Greenberg, Natalie Duerkopp, Ryan O. Emerson & Harlan S. Robins
The vast diversity of B-cell receptors (BCR) and secreted antibodies enables the recognition of, and response to, a wide range of epitopes, but this diversity has also limited our understanding of humoral immunity. We present a public database of more than 37 million unique BCR sequences from three healthy adult donors that is many fold deeper than any existing resource, together with a set of online tools designed to facilitate the visualization and analysis of...

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: A key metabolic gene for recurrent freshwater colonization and radiation in fishes

Asano Ishikawa, Naoki Kabeya, Koki Ikeya, Ryo Kakioka, Jennifer N. Cech, Naoki Osada, Miguel C. Leal, Jun Inoue, Manabu Kume, Atsushi Toyoda, Ayumi Tezuka, Atsushi J. Nagano, Yo Y. Yamasaki, Yuto Suzuki, Tomoyuki Kokita, Hiroshi Takahashi, Kay Lucek, David Marques, Yusuke Takehana, Kiyoshi Naruse, Seiichi Mori, Oscar Monroig, Nemiah Ladd, Carsten J. Schubert, Blake Matthews … & Jun Kitano
Colonization of new ecological niches has triggered large adaptive radiations. Although some lineages have made use of such opportunities, not all do so. The factors causing this variation among lineages are largely unknown. Here, we show that deficiency in docosahexaenoic acid (DHA), an essential ω-3 fatty acid, can constrain freshwater colonization by marine fishes. Our genomic analyses revealed multiple independent duplications of the fatty acid desaturase gene Fads2 in stickleback lineages that subsequently colonized and...

Data from: Demographic history of a recent invasion of house mice on the isolated Island of Gough

Melissa M. Gray, Daniel Wegmann, Ryan J. Haasl, Michael A. White, Sofia I. Gabriel, Jeremy B. Searle, Richard J. Cuthbert, Peter G. Ryan & Bret A. Payseur
Island populations provide natural laboratories for studying key contributors to evolutionary change, including natural selection, population size, and the colonization of new environments. The demographic histories of island populations can be reconstructed from patterns of genetic diversity. House mice (Mus musculus) inhabit islands throughout the globe, making them an attractive system for studying island colonization from a genetic perspective. Gough Island, in the central South Atlantic Ocean, is one of the remotest islands in the...

Data from: Single‐cell profiling screen identifies microtubule‐dependent reduction of variability in signaling

C. Gustavo Pesce, William J. Peria, Stefan Zdraljevic, Daniel Rockwell, Richard C. Yu, Alejandro Colman-Lerner, Roger Brent, Alan Bush & María Victoria Repetto
Populations of isogenic cells often respond coherently to signals, despite differences in protein abundance and cell state. Previously, we uncovered processes in the Saccharomyces cerevisiae pheromone response system (PRS) that reduced cell‐to‐cell variability in signal strength and cellular response. Here, we screened 1,141 non‐essential genes to identify 50 “variability genes”. Most had distinct, separable effects on strength and variability of the PRS, defining these quantities as genetically distinct “axes” of system behavior. Three genes affected...

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: Caenorhabditis elegans genes affecting interindividual variation in life-span biomarker gene expression

Alexander Mendenhall, Matthew M. Crane, Patricia M. Tedesco, Thomas E. Johnson & Roger Brent
Genetically identical organisms grown in homogenous environments differ in quantitative phenotypes. Differences in one such trait, expression of a single biomarker gene, can identify isogenic cells or organisms that later manifest different fates. For example, in isogenic populations of young adult Caenorhabditis elegans, differences in Green Fluorescent Protein (GFP) expressed from the hsp-16.2 promoter predict differences in life span. Thus, it is of interest to determine how interindividual differences in biomarker gene expression arise. Prior...

Data from: Mapping polyclonal HIV-1 antibody responses via next-generation neutralization fingerprinting

Nicole A. Doria-Rose, Han R. Altae-Tran, Ryan S. Roark, Stephen D. Schmidt, Matthew S. Sutton, Mark K. Louder, Gwo-Yu Chuang, Robert T. Bailer, Valerie Cortez, Rui Kong, Krisha McKee, Sijy O'Dell, Felicia Wang, Salim S. Abdool Karim, James M. Binley, Mark Connors, Barton F. Haynes, Malcolm A. Martin, David C. Montefiori, Lynn Morris, Julie Overbaugh, Peter D. Kwong, John R. Mascola, Ivelin S. Georgiev & Sijy O’Dell
Computational neutralization fingerprinting, NFP, is an efficient and accurate method for predicting the epitope specificities of polyclonal antibody responses to HIV-1 infection. Here, we present next-generation NFP algorithms that substantially improve prediction accuracy for individual donors and enable serologic analysis for entire cohorts. Specifically, we developed algorithms for: (a) selection of optimized virus neutralization panels for NFP analysis, (b) estimation of NFP prediction confidence for each serum sample, and (c) identification of sera with potentially...

Data from: Consistency of VDJ rearrangement and substitution parameters enables accurate B cell receptor sequence annotation

Duncan K. Ralph, & Frederick A. Matsen
VDJ rearrangement and somatic hypermutation work together to produce antibody-coding B cell receptor (BCR) sequences for a remarkable diversity of antigens. It is now possible to sequence these BCRs in high throughput; analysis of these sequences is bringing new insight into how antibodies develop, in particular for broadly-neutralizing antibodies against HIV and influenza. A fundamental step in such sequence analysis is to annotate each base as coming from a specific one of the V, D,...

Data from: Adaptive evolution and environmental durability jointly structure phylodynamic patterns in avian influenza viruses

Benjamin Roche, John M. Drake, Justin Brown, David E. Stallknecht, Trevor Bedford & Pejman Rohani
Avian influenza viruses (AIVs) have been pivotal to the origination of human pandemic strains. Despite their scientific and public health significance, however, there remains much to be understood about the ecology and evolution of AIVs in wild birds, where major pools of genetic diversity are generated and maintained. Here, we present comparative phylodynamic analyses of human and AIVs in North America, demonstrating (i) significantly higher standing genetic diversity and (ii) phylogenetic trees with a weaker...

Application of simultaneous selective pressures slows adaptation

Lauren Merlo, Kathleen Sprouffske, Taylor Howard, Kristin Gardiner, Aleah Caulin, Steven Blum, Perry Evans, Antonio Bedalov, Paul Sniegowski & Carlo Maley
Background and objectives: Beneficial mutations that arise in an evolving asexual population may compete or interact in ways that alter the overall rate of adaptation through mechanisms such as clonal or functional interference. The application of multiple selective pressures simultaneously may allow for a greater number of adaptive mutations, increasing the opportunities for competition between selectively advantageous alterations, and thereby reducing the rate of adaptation. Methodology: We evolved a strain of Saccharomyces cerevisiae that could...

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: Evolutionary inferences from the analysis of exchangeability

Andrew P. Hendry, Renaud Kaeuffer, Erika Crispo, Catherine Lynn Peichel & Daniel I. Bolnick
Evolutionary inferences are usually based on statistical models that compare mean genotypes and phenotypes (or their frequencies) among populations. An alternative is to use the actual distribution of genotypes and phenotypes to infer the “exchangeability” of individuals among populations. We illustrate this approach by using discriminant functions on principal components to classify individuals among paired lake and stream populations of threespine stickleback in each of six independent watersheds. Classification based on neutral and non-neutral microsatellite...

Data from: Effective online Bayesian phylogenetics via sequential Monte Carlo with guided proposals

Mathieu Fourment, Brian C. Claywell, Vu Dinh, Connor McCoy, & Aaron E. Darling
Modern infectious disease outbreak surveillance produces continuous streams of sequence data which require phylogenetic analysis as data arrives. Current software packages for Bayesian phylogenetic inference are unable to quickly incorporate new sequences as they become available, making them less useful for dynamically unfolding evolutionary stories. This limitation can be addressed by applying a class of Bayesian statistical inference algorithms called sequential Monte Carlo (SMC) to conduct online inference, wherein new data can be continuously incorporated...

Data from: Developmental mechanisms of stripe patterns in rodents

Ricardo Mallarino, Corneliu Henegar, Mercedes Mirasierra, Marie Manceau, Carsten Schradin, Mario Vallejo, Slobodan Beronja, Gregory S. Barsh & Hopi E. Hoekstra
Mammalian colour patterns are among the most recognizable characteristics found in nature and can have a profound impact on fitness. However, little is known about the mechanisms underlying the formation and subsequent evolution of these patterns. Here we show that, in the African striped mouse (Rhabdomys pumilio), periodic dorsal stripes result from underlying differences in melanocyte maturation, which give rise to spatial variation in hair colour. We identify the transcription factor ALX3 as a regulator...

Data from: Sensory trait variation contributes to biased dispersal of threespine stickleback in flowing water

Yuexin Jiang, Catherine L. Peichel, Fei Ling, Daniel I. Bolnick, Z. Rizvi, S. Thompson, V. V. Palivela & L. Torrance
Gene flow is widely thought to homogenize spatially separate populations, eroding effects of divergent selection. The resulting theory of ‘migration-selection balance’ is predicated on a common assumption that all genotypes are equally prone to dispersal. If instead certain genotypes are disproportionately likely to disperse, then migration can actually promote population divergence. For example, previous work has shown that threespine stickleback (Gasterosteus aculeatus) differ in their propensity to move up- or down-stream (‘rheotactic response’), which may...

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: Minimizing the average distance to a closest leaf in a phylogenetic tree

, Aaron Gallagher, Connor McCoy, Frederick A. Matsen & Connor O. McCoy
When performing an analysis on a collection of molecular sequences, it can be convenient to reduce the number of sequences under consideration while maintaining some characteristic of a larger collection of sequences. For example, one may wish to select a subset of high-quality sequences that represent the diversity of a larger collection of sequences. One may also wish to specialize a large database of characterized “reference sequences” to a smaller subset that is as close...

Ancient viral genomes reveal introduction of HBV and B19V into Mexico during the transatlantic slave trade

Daniel Blanco-Melo & Maria Avila-Arcos
After the European colonization of the Americas there was a dramatic population collapse of the Indigenous inhabitants caused in part by the introduction of new pathogens. Although there is much speculation on the etiology of the Colonial epidemics, direct evidence for the presence of specific viruses during the Colonial era is lacking. To uncover the diversity of viral pathogens during this period, we designed an enrichment assay targeting ancient DNA (aDNA) from viruses of clinical...

Phosphotyrosine peptide abundance in control and Cul5-deficient MCF10A cells

Jonathan Cooper
The Cullin 5 RING ligase complex inhibits Src activity and Src-dependent transformation of MCF10A epithelial cells, in part by targeting pY proteins such as pYCas for degradation by the ubiquitin-proteasome system (Teckchandani et al., 2014). Because overexpression of Cas alone did not phenocopy CRL5 inhibition (Teckchandani et al., 2014), we infer that CRL5 down-regulates additional pY proteins that become limiting when Cas is over-expressed. We sought to identify such pY proteins by screening for pY...

Data from: Arabidopsis hybrid speciation processes

Roswitha Schmickl & Marcus A. Koch
The genus Arabidopsis provides a unique opportunity to study fundamental biological questions in plant sciences utilizing the diploid model species A. thaliana and A. lyrata. However, only a few studies have focused on introgression and hybrid speciation in Arabidopsis, although polyploidy is a common phenomenon within this genus. More recently, there is growing evidence of significant gene flow between the various Arabidopsis species. So far, we know A. suecica and A. kamchatica as fully stabilized...

Data from: Admixture mapping of male nuptial color and body shape in a recently formed hybrid population of threespine stickleback

Tiffany B. Malek, Janette W. Boughman, Ian Dworkin & Catherine L. Peichel
Despite recent progress, we still know relatively little about the genetic architecture that underlies adaptation to divergent environments. Determining whether the genetic architecture of phenotypic adaptation follows any predictable patterns requires data from a wide variety of species. However, in many organisms, genetic studies are hindered by the inability to perform genetic crosses in the laboratory or by long generation times. Admixture mapping is an approach that circumvents these issues by taking advantage of hybridization...

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...

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