48 Works

Data from: Repeated losses of PRDM9-directed recombination despite the conservation of PRDM9 across vertebrates

Zachary Baker, Molly Schumer, Yuki Haba, Lisa Bashkirova, Chris Holland, Gil G Rosenthal & Molly Przeworski
Studies of highly diverged species have revealed two mechanisms by which meiotic recombination is directed to the genome—through PRDM9 binding or by targeting promoter-like features—that lead to dramatically different evolutionary dynamics of hotspots. Here, we identify PRDM9 orthologs from genome and transcriptome data in 225 species. We find the complete PRDM9 ortholog across distantly related vertebrates but, despite this broad conservation, infer a minimum of six partial and three complete losses. Strikingly, taxa carrying the...

Data from: Ranking and characterization of established BMI and lipid associated loci as candidates for gene-environment interactions

Dmitry Shungin, Wei Q. Deng, Tibor V. Varga, Jian'an Luan, Evelin Mihailov, Andres Metspalu, Andrew P. Morris, Nita G. Forouhi, Cecilia Lindgren, Patrik K. E. Magnusson, Nancy L. Pedersen, Göran Hallmans, Audrey Y. Chu, Anne E. Justice, Mariaelisa Graff, Thomas W. Winkler, Lynda M. Rose, Claudia Langenberg, L. Adrienne Cupples, Paul M. Ridker, Nicholas J. Wareham, Ken K. Ong, Ruth J. F. Loos, Daniel I. Chasman, Erik Ingelsson … & Paul W. Franks
Phenotypic variance heterogeneity across genotypes at a single nucleotide polymorphism (SNP) may reflect underlying gene-environment (G·E) or gene-gene interactions. We modeled variance heterogeneity for blood lipids and BMI in up to 44,211 participants and investigated relationships between variance effects (Pv), G·E interaction effects (with smoking and physical activity), and marginal genetic effects (Pm). Correlations between Pv and Pm were stronger for SNPs with established marginal effects (Spearman's ρ=0.401 for triglycerides, and ρ=0.236 for BMI) compared...

Data from: Temporal specificity of the initial adaptive response in motor adaptation

Wilsaan M. Joiner, Gary C. Sing & Maurice A. Smith
Repeated exposure to a novel physical environment eventually leads to a mature adaptive response whereby feedforward changes in motor output mirror both the amplitude and temporal structure of the environmental perturbations. However, adaptive responses at the earliest stages of learning have been found to be not only smaller, but systematically less specific in their temporal structure compared to later stages of learning. This observation has spawned a lively debate as to whether the temporal structure...

Data from: Habitat patterns in tropical rain forests: a comparison of 105 plots in northwest Borneo

Matthew D. Potts, Peter S. Ashton, Les S. Kaufman & Joshua B. Plotkin
Understanding the maintenance of high tropical tree species diversity requires disentangling the effects of habitat vs. geographic distance. Using floristic, topographic, and soil nutrient data from 105 0.6-ha plots in mixed dipterocarp forest throughout Sarawak, Malaysian Borneo, we explore the degree to which floristic patterns are habitat-driven from local to landscape scales. We assess how the floristic influence of geographic distance vs. abiotic factors varies from local to regional scales. We employ several multivariate analytical...

Data from: Edge effects on components of diversity and above-ground biomass in a tropical rainforest

Onja H. Razafindratsima, Kerry A. Brown, Fabio Carvalho, Steig E. Johnson, Patricia C. Wright & Amy E. Dunham
1. Edge effects are among the most significant consequences of forest fragmentation. Therefore, understanding the impacts of edge creation on biodiversity is crucial for forest management and biological conservation. 2. In this study, we used trait-based and phylogenetic approaches to examine the effects of fragmentation on components of diversity and above-ground biomass of rainforest tree communities in Madagascar in forest edge vs. interior habitats. 3. Tree communities in forest edges showed lower phylogenetic diversity relative...

Data from: Spatially explicit analysis sheds new light on the Pleistocene megafaunal extinction in North America

Meaghan M. Emery-Wetherell, Brianna K. McHorse & Edward Byrd Davis
The late Pleistocene megafaunal extinctions may have been the first extinctions directly related to human activity, but in North America the close temporal proximity of human arrival and the Younger Dryas climate event has hindered efforts to identify the ultimate extinction cause. Previous work evaluating the roles of climate change and human activity in the North American megafaunal extinction has been stymied by a reliance on geographic binning, yielding contradictory results among researchers. We used...

Data from: Genomic evidence of gene flow during reinforcement in Texas Phlox

Federico Roda, Fábio K. Mendes, Matthew W. Hahn & Robin Hopkins
Gene flow can impede the evolution of reproductive isolating barriers between species. Reinforcement is the process by which pre-zygotic reproductive isolation evolves in sympatry due to selection to decrease costly hybridization. It is known that reinforcement can be prevented by too much gene flow, but we still do not know how often have pre-zygotic barriers evolved in the presence of gene flow or how much gene flow can occur during reinforcement. Flower color divergence in...

Data from: Origins of lymphatic and distant metastases in human colorectal cancer

Kamila Naxerova, Johannes G. Reiter, Elena Brachtel, Jochen K. Lennerz, Marc Van De Wetering, Andrew Rowan, Tianxi Cai, Hans Clevers, Charles Swanton, Martin A. Nowak, Stephen J. Elledge & Rakesh K. Jain
The spread of cancer cells from primary tumors to regional lymph nodes is often associated with reduced survival. One prevailing model to explain this association posits that fatal, distant metastases are seeded by lymph node metastases. This view provides a mechanistic basis for the TNM staging system and is the rationale for surgical resection of tumor-draining lymph nodes. Here we examine the evolutionary relationship between primary tumor, lymph node, and distant metastases in human colorectal...

Data from: Early photosynthetic eukaryotes inhabited low-salinity habitats

Patricia Sánchez-Baracaldo, John A. Raven, Davide Pisani & Andrew H. Knoll
The early evolutionary history of the chloroplast lineage remains an open question. It is widely accepted that the endosymbiosis that established the chloroplast lineage in eukaryotes can be traced back to a single event, in which a cyanobacterium was incorporated into a protistan host. It is still unclear, however, which Cyanobacteria are most closely related to the chloroplast, when the plastid lineage first evolved, and in what habitats this endosymbiotic event occurred. We present phylogenomic...

Data from: Outlier analyses to test for local adaptation to breeding grounds in a migratory arctic seabird

Anna Tigano, Allison J. Shultz, Scott V. Edwards, Gregory J. Robertson & Vicki L. Friesen
Investigating the extent (or the existence) of local adaptation is crucial to understanding how populations adapt. When experiments or fitness measurements are difficult or impossible to perform in natural populations, genomic techniques allow us to investigate local adaptation through the comparison of allele frequencies and outlier loci along environmental clines. The thick-billed murre (Uria lomvia) is a highly philopatric colonial arctic seabird that occupies a significant environmental gradient, shows marked phenotypic differences among colonies, and...

Data from: Induced parental care in a poison frog: a tadpole cross-fostering experiment

Andrius Pašukonis, Kristina Barbara Beck, Marie-Therese Fischer, Steffen Weinlein, Susanne Stückler & Eva Ringler
Understanding the external stimuli and natural contexts that elicit complex behaviours, such as parental care, is key in linking behavioural mechanisms to their real-life function. Poison frogs provide obligate parental care by shuttling their tadpoles from terrestrial clutches to aquatic nurseries, but little is known about the proximate mechanisms that control these behaviours. In this study, we used Allobates femoralis, a poison frog with predominantly male parental care, to investigate whether tadpole transport can be...

Data from: Excavation and aggregation as organizing factors in de novo construction by mound-building termites

Ben Green, Paul Bardunias, J. Scott Turner, Radhika Nagpal & Justin Werfel
Termites construct complex mounds that are orders of magnitude larger than any individual and fulfil a variety of functional roles. Yet the processes through which these mounds are built, and by which the insects organize their efforts, remain poorly understood. The traditional understanding focuses on stigmergy, a form of indirect communication in which actions that change the environment provide cues that influence future work. Termite construction has long been thought to be organized via a...

Data from: Genomic footprints of adaptation in a cooperatively breeding tropical bird across a vegetation gradient

Flavia Termignoni-Garcia, Juan P. Jaramillo-Correa, Juan Chablé-Santos, Mark Liu, Allison J. Shultz, Scott V. Edwards, Patricia Escalante Pliego & Patricia Escalante-Pliego
Identifying the genetic basis of phenotypic variation and its relationship with the environment is key to understanding how local adaptations evolve. Such patterns are especially interesting among populations distributed across habitat gradients, where genetic structure can be driven by isolation by distance (IBD) and/or isolation by environment (IBE). Here, we used variation in ~1,600 high-quality SNPs derived from paired-end sequencing of double-digest restriction site-associated DNA (ddRAD-Seq) to test hypotheses related to IBD and IBE in...

Data from: Ecophysiological variation across a forest-ecotone gradient produces divergent climate change vulnerability within species

Félix Landry Yuan, Adam H. Freedman, Laurent Chirio, Matthew LeBreton & Timothy C. Bonebrake
Climate change related risks and impacts on ectotherms will be mediated by habitats and their influence on local thermal environments. While many studies have documented morphological and genetic aspects of niche divergence across habitats, few have examined thermal performance across such gradients and directly linked this variation to contemporary climate change impacts. In this study, we quantified variation in thermal performance across a gradient from forest to gallery forest-savanna mosaic in Cameroon for a skink...

Data from: Use of a microfluidic platform to uncover basic features of energy and environmental stress responses in individual cells of Bacillus subtilis

Matthew T. Cabeen, Jonathan R. Russell, Johan Paulsson & Richard Losick
Bacteria use a variety of stress-sensing systems to sense and respond to diverse stressors and to ensure their survival under adverse conditions. The gram-positive bacterium Bacillus subtilis responds to energy stress (ATP depletion) and to environmental stressors using two distinct stress-sensing pathways that converge on the alternative sigma factor σB to provoke a general stress response. Past efforts to study the σB stress response in bulk culture and on agarose pads were unable to visualize...

Data from: Genetic drift and selection in many-allele range expansions

Bryan T. Weinstein, Maxim O. Lavrentovich, Wolfram Moebius, Andrew W. Murray, David R. Nelson & Wolfram Möbius
We experimentally and numerically investigate the evolutionary dynamics of four competing strains of E. coli with differing expansion velocities in radially expanding colonies. We compare experimental measurements of the average fraction, correlation functions between strains, and the relative rates of genetic domain wall annihilations and coalescences to simulations modeling the population as a one-dimensional ring of annihilating and coalescing random walkers with deterministic biases due to selection. The simulations reveal that the evolutionary dynamics can...

Data from: Aneuploidy causes non-genetic individuality

Rebecca R. Beach, Chiara Ricci-Tam, Christopher M. Brennan, Christine A. Moomau, Pei-Hsin Hsu, Bo Hua, Rebecca E. Silberman, Michael Springer & Angelika Amon
Phenotypic variability is a hallmark of diseases involving chromosome gains and losses, such as Down syndrome and cancer. Allelic variances have been thought to be the sole cause of this heterogeneity. Here, we systematically examine the consequences of gaining and losing single or multiple chromosomes to show that the aneuploid state causes non-genetic phenotypic variability. Yeast cell populations harboring the same defined aneuploidy exhibit heterogeneity in cell-cycle progression and response to environmental perturbations. Variability increases...

Data from: Genomic clustering of adaptive loci during parallel evolution of an Australian wildflower

Federico Roda, Greg M. Walter, Rick Nipper & Daniel Ortiz-Barrientos
The buildup of the phenotypic differences that distinguish species has long intrigued biologists. These differences are often inherited as stable polymorphisms that allow the co-segregation of adaptive variation within species, and facilitate the differentiation of complex phenotypes between species. It has been suggested that the clustering of adaptive loci could facilitate this process but evidence is still scarce. Here we used QTL analysis to study the genetic basis of phenotypic differentiation between coastal populations of...

Data from: Epigenetic memory via concordant DNA methylation is inversely correlated to developmental potential of mammalian cells

Minseung Choi, Diane P. Genereux, Jamie Goodson, Haneen Al-Azzawi, Shannon Q. Allain, Noah Simon, Stan Palasek, Carol B. Ware, Chris Cavanaugh, Daniel G. Miller, Winslow C. Johnson, Kevin D. Sinclair, Reinhard Stöger & Charles D. Laird
In storing and transmitting epigenetic information, organisms must balance the need to maintain information about past conditions with the capacity to respond to information in their current and future environments. Some of this information is encoded by DNA methylation, which can be transmitted with variable fidelity from parent to daughter strand. High fidelity confers strong pattern matching between the strands of individual DNA molecules and thus pattern stability over rounds of DNA replication; lower fidelity...

Data from: Centennial-scale reductions in nitrogen availability in temperate forests of the United States

K. K. McLauchlan, L. M. Gerhart, J. J. Battles, J. M. Craine, A. J. Elmore, P. E. Higuera, M. C. Mack, B. E. McNeil, D. M. Nelson, N. Pederson & S. S. Perakis
Forests cover 30% of the terrestrial Earth surface and are a major component of the global carbon (C) cycle. Humans have doubled the amount of global reactive nitrogen (N), increasing deposition of N onto forests worldwide. However, other global changes—especially climate change and elevated atmospheric carbon dioxide concentrations—are increasing demand for N, the element limiting primary productivity in temperate forests, which could be reducing N availability. To determine the long-term, integrated effects of global changes...

Data from: Chaos and the (un)predictability of evolution in a changing environment

Artur Rego Costa, Florence Débarre, Luis-Miguel Chevin & Artur Rego-Costa
Among the factors that may reduce the predictability of evolution, chaos, characterized by a strong dependence on initial conditions, has received much less attention than randomness due to genetic drift or environmental stochasticity. It was recently shown that chaos in phenotypic evolution arises commonly under frequency-dependent selection caused by competitive interactions mediated by many traits. This result has been used to argue that chaos should often make evolutionary dynamics unpredictable. However, populations also evolve largely...

Data from: Polygyny does not explain the superior competitive ability of dominant ant associates in the African ant-plant, Acacia (Vachellia) drepanolobium

John H. Boyle, Dino J. Martins, Julianne Pelaez, Paul M. Musili, Staline Kibet, S. Kimani Ndung'u, David Kenfack & Naomi E. Pierce
1. The Acacia drepanolobium (also known as Vachellia drepanolobium) ant-plant symbiosis is considered a classic case of species coexistence, in which four species of tree-defending ants compete for nesting space in a single host tree species. Coexistence in this system has been explained by trade-offs in the ability of the ant associates to compete with each other for occupied trees versus the ability to colonize unoccupied trees. 2. We seek to understand the proximal reasons...

Data from: Winter storms drive rapid phenotypic, regulatory and genomic shifts in the green anole lizard

Shane C. Campbell-Staton, Zachary A. Cheviron, Nicholas Rochette, Julian Catchen, Jonathan B. Losos & Scott V. Edwards
Extreme environmental perturbations offer opportunities to observe the effects of natural selection in wild populations. During the winter of 2013–2014, the southeastern United States endured an extreme cold event. We used thermal performance, transcriptomics, and genome scans to measure responses of lizard populations to storm-induced selection. We found significant increases in cold tolerance at the species’ southern limit. Gene expression in southern survivors shifted toward patterns characteristic of northern populations. Comparing samples before and after...

Data from: How environmental conditions shape the chemical signal design of lizards

Simon Baeckens, José Martín, Roberto García-Roa, Panayiotis Pafilis, Katleen Huyghe & Raoul Van Damme
1. The signals that animals use to communicate often differ considerably among species. Part of this variation in signal design may derive from differential natural selection on signal efficacy; the ability of the signal to travel efficiently through the environment and attract the receiver’s attention. For the visual and acoustic modalities, the effect of the physical environment on signal efficacy is a well-studied selective force. Still, very little is known on its impact on the...

Data from: Sexual imprinting and speciation in two Peromyscus species

Emily Kay Delaney & Hopi E. Hoekstra
Sexual isolation, a reproductive barrier, can prevent interbreeding between diverging populations or species. Sexual isolation can have a clear genetic basis; however, it may also result from learned mate preferences that form via sexual imprinting. Here, we demonstrate that two sympatric sister species of mice—the white-footed mouse (Peromyscus leucopus) and its closest relative, the cotton mouse (P. gossypinus)—hybridize only rarely in the wild despite co-occurring in the same habitat and lack of any measurable intrinsic...

Registration Year

  • 2017

Resource Types

  • Dataset


  • Harvard University
  • University of Montana
  • Massachusetts Institute of Technology
  • National Museum
  • Rice University
  • Princeton University
  • University of Michigan-Ann Arbor
  • University of Queensland
  • University of North Carolina
  • University of California, Berkeley