76 Works

Data from: Assembly and ecological function of the root microbiome across angiosperm plant species

Connor R. Fitzpatrick, Julia Copeland, Pauline W. Wang, David S. Guttman, Peter M. Kotanen & Marc T. J. Johnson
Across plants and animals, host-associated microbial communities play fundamental roles in host nutrition, development, and immunity. The factors that shape host–microbiome interactions are poorly understood, yet essential for understanding the evolution and ecology of these symbioses. Plant roots assemble two distinct microbial compartments from surrounding soil: the rhizosphere (microbes surrounding roots) and the endosphere (microbes within roots). Root-associated microbes were key for the evolution of land plants and underlie fundamental ecosystem processes. However, it is...

Data from: Genetic basis to hybrid inviability is more complex than hybrid male sterility in Caenorhabditis nematodes

Joanna D. Bundus, Donglin Wang & Asher D. Cutter
Hybrid male sterility often evolves before female sterility or inviability of hybrids, implying that the accumulation of divergence between separated lineages should lead hybrid male sterility to have a more polygenic basis. However, experimental evidence is mixed. Here, we use the nematodes Caenorhabditis remanei and C. latens to characterize the underlying genetic basis of asymmetric hybrid male sterility and hybrid inviability. We demonstrate that hybrid male sterility is consistent with a simple genetic basis, involving...

Data from: Cooperation and coexpression: how coexpression networks shift in response to multiple mutualists

Sathvik X. Palakurty, John R. Stinchcombe & Michelle E. Afkhami
A mechanistic understanding of community ecology requires tackling the nonadditive effects of multispecies interactions, a challenge that necessitates integration of ecological and molecular complexity-- namely moving beyond pairwise ecological interaction studies and the ‘gene at a time’ approach to mechanism. Here, we investigate the consequences of multispecies mutualisms for the structure and function of genome-wide coexpression networks for the first time, using the tractable and ecologically-important interaction between legume Medicago truncatula, rhizobia, and mycorrhizal fungi....

Data from: Assessment of plasma proteomics biomarker’s ability to distinguish benign from malignant lung nodules

Gerard A. Silvestri, Nichole T. Tanner, Paul Kearney, Anil Vachani, Pierre P. Massion, Alexander Porter, Steven C. Springmeyer, Kenneth C. Fang, David Midthun, Peter J. Mazzone, D. Madtes, J. Landis, A. Levesque, K. Rothe, M. Balaan, B. Dimitt, B. Fortin, N. Ettinger, A. Pierre, L. Yarmus, K. Oakjones-Burgess, N. Desai, Z. Hammoud, A. Sorenson, R. Murali … & F. Allison
Background: Lung nodules are a diagnostic challenge, with an estimated yearly incidence of 1.6 million in the United States. This study evaluated the accuracy of an integrated proteomic classifier in identifying benign nodules in patients with a pretest probability of cancer (pCA) ≤ 50%. Methods: A prospective, multicenter observational trial of 685 patients with 8- to 30-mm lung nodules was conducted. Multiple reaction monitoring mass spectrometry was used to measure the relative abundance of two...

Data from: Faunal overview of the Mud Hill locality from the early Permian Vale Formation of Taylor County, Texas

Bryan M. Gee, Steve J. Rosscoe, Diane Scott, Judie Ostlien & Robert R. Reisz
The Texas red beds represent one of the richest series of early Permian deposits in the world. In particular, the Clear Fork Group has produced a diverse assemblage of temnospondyls, early reptiles, and synapsids. However, most of this material has been sourced from the oldest member, the Arroyo Formation, and the understanding of the paleoecosystem of the younger Vale and Choza Formations is less well-resolved. Here we present a new Vale locality, the first vertebrate-bearing...

Data from: Thermal niche evolution across replicated Anolis lizard adaptive radiations

Alex R. Gunderson, D. Luke Mahler & Manuel Leal
Elucidating how ecological and evolutionary mechanisms interact to produce and maintain biodiversity is a fundamental problem in evolutionary ecology. We investigate this issue by focusing on how physiological evolution affects performance and species coexistence along the thermal niche axis in replicated radiations of Anolis lizards, groups best known for resource partitioning based on morphological divergence. We find repeated divergence in thermal physiology within these radiations, and that this divergence significantly affects performance within natural thermal...

Data from: A new small captorhinid reptile from the lower Permian of Oklahoma and resource partitioning among small captorhinids in the Richards Spur fauna

Sean P. Modesto, Diane Scott & Robert R. Reisz
Two partial reptile skulls and six dentigerous fragments from the lower Permian Richards Spur locality of Oklahoma represent a new genus and species of small captorhinid reptile. Labidosauriscus richardi gen. et sp. nov. is distinguished from other captorhinids in the reduction of the height of the ridges forming the characteristic net-like, ridge-and-pit cranial sculpturing of captorhinids, and the superimposition of a system of finer pits and furrows over the primary ridge-and-pit cranial ornamentation. Labidosauriscus richardi...

Data from: Competition for mates and the improvement of nonsexual fitness

Li Yun, Patrick J. Chen, Kevin E. Kwok, Christopher S. Angell, Howard D. Rundle & Aneil F. Agrawal
Competition for mates can be a major source of selection, not just on secondary sexual traits but across the genome. Mate competition strengthens selection on males via sexual selection, which typically favours healthy, vigorous individuals and, thus, all genetic variants that increase overall quality. However, recent studies suggest another major effect of mate competition that could influence genome-wide selection: sexual harassment by males can drastically weaken selection on quality in females. Because of these conflicting...

Data from: Habitat connectivity is determined by the scale of habitat loss and dispersal strategy

Allan H. Edelsparre, Ashif Shahid & Mark J. Fitzpatrick
Understanding factors that ameliorate the impact of habitat loss is a major focus of conservation research. One key factor influencing species persistence and evolution is the ability to disperse across increasingly patchy landscapes. Here we ask whether interpatch distance (a proxy for habitat loss) and dispersal strategy can interact to form thresholds where connectivity breaks down. We assayed dispersal across a range of interpatch distances in fruit flies carrying allelic variants of a gene known...

Data from: The UBR-1 ubiquitin ligase regulates glutamate metabolism to generate coordinated motor pattern in Caenorhabditis elegans

Jysothna Chitturi, Wesley Hung, Anas M. Abdel Rahman, Min Wu, Maria A. Lim, John Calarco, Rene Baran, Xun Huang, James W. Dennis, Mei Zhen & Jyothsna Chitturi
UBR1 is an E3 ubiquitin ligase best known for its ability to target protein degradation by the N-end rule. The physiological functions of UBR family proteins, however, remain not fully understood. We found that the functional loss of C. elegans UBR-1 leads to synchronized motor neuron activation, preventing body bending when animals generate reversal movements. This motor deficit is rescued by removing GOT-1, a transaminase that converts aspartate to glutamate. Both UBR-1 and GOT-1 are...

Data from: Selection for pollen competitive ability in mixed-mating systems

Madeline Amanda Erzen Peters & Arthur E. Weis
Co-expression of genes in plant sporophytes and gametophytes allows correlated gametic and sporophytic selection. Theory predicts that, under outcrossing, an allele conferring greater pollen competitive ability should fix within a population unless antagonistic pleiotropy with the sporophyte stage is strong. However, under strong selfing, pollen competitiveness is immaterial as superior and inferior competitors are deposited on opposite stigmas, producing assortative competition. Because many plant species have mixed-mating systems, selfing should be critical in the spread...

Data from: An updated gene atlas for maize reveals organ-specific and stress-induced genes

Genevieve M. Hoopes, John P. Hamilton, Joshua C. Wood, Eddi Esteban, Asher Pasha, Brieanne Vaillancourt, Nicholas J. Provart & C. Robin Buell
Maize(Zea mays L.), a model species for genetic studies, is one of the two most important crop species worldwide.The genome sequence of the reference genotype, B73, representative of the stiff stalk heterotic group was recently updated (AGPv4) using long‐read sequencing and optical mapping technology. To facilitate the use of AGPv4 and to enable functional genomic studies and association of genotype with phenotype, we determined expression abundances for replicated mRNA‐sequencing datasets from 79 tissues and five...

Data from: C4 anatomy can evolve via a single developmental change

Marjorie R. Lundgren, Luke T. Dunning, Jill K. Olofsson, Jose J. Moreno Villena, Jacques W. Bouvier, Tammy L. Sage, Roxana Khosravesh, Stefanie Sultmanis, Matt Stata, Brad S. Ripley, Maria S. Vorontsova, Guillaume Besnard, Claire Adams, Nicholas Cuff, Anthony Mapaura, Matheus E. Bianconi, Christine M. Long, Pascal-Antoine Christin, Colin P. Osborne, Roxana Khoshravesh & Jose J. Moreno-Villena
C4 photosynthesis boosts productivity in warm environments. Paradoxically, this complex physiological process evolved independently in numerous plant lineages, despite requiring specialized leaf anatomy. The anatomical modifications underlying C4 evolution have previously been evaluated through interspecific comparisons, which capture numerous changes besides those needed for C4 functionality. Here, we quantify the anatomical changes accompanying the transition between non-C4 and C4 phenotypes by sampling widely across the continuum of leaf anatomical traits in the grass Alloteropsis semialata....

Data from: Divergent selection on the biomechanical properties of stamens under wind and insect pollination

David Timerman, Spencer C.H. Barrett & Spencer C. H. Barrett
Wind pollination has evolved from insect pollination in numerous angiosperm lineages and is associated with a characteristic syndrome of morphological traits. The traits initiating transitions to wind pollination and the ecological drivers involved are poorly understood. Here, we examine this problem in Thalictrum pubescens, an ambophilous (insect and wind pollination) species that probably represents a transitional state in the evolution of wind pollination in some taxa. We investigated wind-induced pollen release by forced harmonic motion...

Data from: An experimental test of the mutation-selection balance model for the maintenance of genetic variance in fitness components

Nathaniel P. Sharp & Aneil F. Agrawal
Despite decades of research, the factors that maintain genetic variation for fitness are poorly understood. It is unclear what fraction of the variance in a typical fitness component can be explained by mutation-selection balance and whether fitness components differ in this respect. In theory, the level of standing variance in fitness due to mutation-selection balance can be predicted using the rate of fitness decline under mutation accumulation, and this prediction can be directly compared to...

Data from: Modern spandrels: the roles of genetic drift, gene flow and natural selection in the formation of parallel clines

James S. Santangelo, Marc T.J. Johnson & Rob W. Ness
Urban environments offer the opportunity to study the role of adaptive and non-adaptive evolutionary processes on an unprecedented scale. While the presence of parallel clines in heritable phenotypic traits is often considered strong evidence for the role of natural selection, non-adaptive evolutionary processes can also generate clines, and this may be more likely when traits have a non-additive genetic basis due to epistasis. In this paper, we use spatially-explicit simulations modelled according to the cyanogenesis...

Data from: The ‘filtering’ metaphor revisited: competition and environment jointly structure invasibility and coexistence

Rachel M. Germain, Margaret M. Mayfield & Benjamin Gilbert
‘Filtering’, or the reduction in species diversity that occurs because not all species can persist in all locations, is thought to unfold hierarchically, controlled by the environment at large scales and competition at small scales. However, the ecological effects of competition and the environment are not independent, and observational approaches preclude investigation into their interplay. We use a demographic approach with 30 plant species to experimentally test (i) the effect of competition on species persistence...

Data from: The effects of haploid selection on Y chromosome evolution in two closely related dioecious plants

George Sandler, Felix E.G. Beaudry, Spencer C.H. Barrett, Stephen I. Wright, Felix E. G. Beaudry & Spencer C. H. Barrett
The evolution of sex chromosomes is usually considered to be driven by sexually antagonistic selection in the diploid phase. However, selection during the haploid gametic phase of the lifecycle has recently received theoretical attention as possibly playing a central role in sex chromosome evolution, especially in plants where gene expression in the haploid phase is extensive. In particular, male-specific haploid selection might favour the linkage of pollen beneficial alleles to male sex determining regions on...

Data from: Habitat partitioning during character displacement between the sexes

Stephen P. De Lisle, Samuel Paiva & Locke Rowe
Ecological differences between the sexes are often interpreted as evidence of within-species ecological character displacement (ECD), a hypothesis with almost no direct tests. Here we experimentally-test two predictions, that are direct corollaries of ECD between the sexes, in a salamander. First, we find support for the prediction that each sex has a growth rate advantage in the aquatic microhabitat where it is most commonly found. Second, we test the prediction that selection for ECD in...

Data from: Testing for latitudinal gradients in defense at the macroevolutionary scale

Daniel N. Anstett, Jeffery R. Ahern, Marc T.J. Johnson, Juha-Pekka Salminen & Jeffrey R. Ahern
Plant defences against herbivores are predicted to evolve to be greater in warmer climates, such as lower latitudes where herbivore pressure is also thought to be higher. Instead, recent findings are often inconsistent with this expectation, suggesting alternative hypotheses are needed. We tested for latitudinal gradients in plant defence evolution at the macroevolutionary scale by characterizing plant chemical defences across 80 species of the evening primroses, spanning both North and South America. We quantified phenolics...

Data from: Virtual endocasts of fossil Sciuroidea: brain size reduction in the evolution of fossoriality

Ornella C. Bertrand, Farrah Amador-Mughal, Madlen M. Lang & Mary T. Silcox
Aplodontia rufa (Mountain Beaver) is the only extant member of Aplodontidae. The fossil record indicates that this family displayed greater taxonomic and ecological diversity in the past, and that the burrowing adaptations of Aplodontia might be derived. We describe the first virtual endocasts of A. rufa and of three fossil aplodontids: Prosciurus relictus and Pros. aff. saskatchewaensis (Early Oligocene), and Mesogaulus paniensis (late Miocene). Our results show that the endocasts of early aplodontid rodents are...

Data from: The European Paromomyidae (Primates, Mammalia): taxonomy, phylogeny, and biogeographic implications

Sergi López-Torres & Mary T. Silcox
Plesiadapiforms represent the first radiation of Primates, appearing near the Cretaceous-Paleogene boundary. Eleven families of plesiadapiforms are recognized, including the Paromomyidae. Four species of paromomyids from the early Eocene have been reported from Europe: Arcius fuscus, Arcius lapparenti, and Arcius rougieri from France, and Arcius zbyszewskii from Portugal. Other Arcius specimens from the early Eocene are known from Masia de l’Hereuet (Spain), Abbey Wood (England), and Sotteville-sur-Mer (Normandy, France). A cladistic analysis of the European...

Data from: Contemporary pollen flow as a multiscale process: evidence from the insect-pollinated herb, Pulsatilla vulgaris

Michelle F. DiLeo, Rolf Holderegger & Helene H. Wagner
1. Understanding the drivers and spatial scale of gene flow is essential for the management of species living in fragmented landscapes. In plants, contemporary pollen flow is typically modeled as a single spatial process, with pollen flow declining exponentially within a short distance of mother plants. However, growing evidence suggests that many species do not conform to this patterns, often showing an excess of long-distance dispersal events or sometimes even multimodality in dispersal kernels. This...

Data from: Integrating morphology and kinematics in the scaling of hummingbird hovering metabolic rate and efficiency

Derrick J.E. Groom, M. Cecilia B. Toledo, Donald R. Powers, Bret W. Tobalske, , Derrick J. E. Groom & Kenneth C. Welch
Wing kinematics and morphology are influential upon the aerodynamics of flight. However, there is a lack of studies linking these variables to metabolic costs, particularly in the context of morphological adaptation to body size. Furthermore, the conversion efficiency from chemical energy into movement by the muscles (mechanochemical efficiency) scales with mass in terrestrial quadrupeds, but this scaling relationship has not been demonstrated within flying vertebrates. Positive scaling of efficiency with body size may reduce the...

Data from: The rise of health biotechnology research in Latin America: a scientometric analysis of health biotechnology production and impact in Argentina, Brazil, Chile, Colombia, Cuba and Mexico.

Dante Israel León-De La O, Halla Thorsteinsdóttir & José Victor Calderón-Salinas
This paper analyzes the patterns of health biotechnology publications in six Latin American countries from 2001 to 2015. The countries studied were Argentina, Brazil, Chile, Colombia, Cuba and Mexico. Before our study, there were no data available on HBT development in half of the Latin-American countries we studied, i.e., Argentina, Colombia and Chile. To include these countries in a scientometric analysis of HBT provides fuller coverage of HBT development in Latin America. The scientometric study...

Registration Year

  • 2018

Resource Types

  • Dataset


  • University of Toronto
  • University of British Columbia
  • University of Washington
  • University of Minnesota
  • Fisheries and Oceans Canada
  • Duke University
  • University of Queensland
  • University of California, San Diego
  • Carleton University
  • Colorado State University