151 Works

Data from: Assessing biological factors affecting post-speciation introgression

Jennafer Hamlin, Mark Hibbins & Leonie Moyle
An increasing number of phylogenomic studies have documented a clear ‘footprint’ of post-speciation introgression among closely-related species. Nonetheless, systematic genome-wide studies of factors that determine the likelihood of introgression remain rare. Here, we propose an a priori hypothesis-testing framework that uses introgression statistics—including a new metric of estimated introgression, Dp —to evaluate general patterns of introgression prevalence and direction across multiple closely related species. We demonstrate this approach using whole genome sequences from 32 lineages...

Narrating the professional self

Maria Shardakova
This presentation examines Russian Flagship students’ personal statements as they (the statements) evolve and change over time to reflect the students’ developing subject positions and group identities. The narrative approach that has been adopted by organizational studies (Gabriel, 2017; Schreyögg, 2005; Tirvassen, 2018) helps demonstrate how students construct the institution of the Language Flagship and their experience of it. Given that cultivating the next generation of global professionals is the primary mission of the Language...

Data from: Regulators of an ancient polyphenism evolved through episodic protein divergence and parallel gene radiations

Erik Ragsdale & Joseph Biddle
Polyphenism is a form of developmental plasticity that transduces environmental cues into discontinuous, often disparate phenotypes. In some cases, polyphenism has been attributed to facilitating morphological diversification and even the evolution of novel traits. However, this process is predicated on the origins and evolutionary maintenance of genetic mechanisms that specify alternate developmental networks. When and how regulatory loci arise and change, specifically before and throughout the history of a polyphenism, is little understood. Here, we...

Dairy Dialogue Map

Colby Vorland, Andrew Brown & David Allison

MonaLog: a Lightweight System for Natural Language Inference Based on Monotonicity

Hai Hu, Qi Chen, Kyle Richardson, Atreyee Mukherjee, Lawrence S. Moss & Sandra Kübler

Herbivore-mediated negative frequency-dependent selection underlies a trichome dimorphism in nature

Jay Goldberg, Curtis Lively, Genevieve Pintel, Sonya Sternlieb, J. Hare, Michael Morrissey & Lynda Delph
Negative frequency-dependent selection (NFDS) has been shown to maintain polymorphism in a diverse array of traits. The action of NFDS has been confirmed through modelling, experimental approaches, and genetic analyses. In this study, we investigated NFDS in the wild using morph-frequency changes spanning a 20-year period from over 30 dimorphic populations of Datura wrightii. In these populations plants either possess glandular (sticky) or non-glandular (velvety) trichomes, and the ratio of these morphs varies substantially among...

Multi-dimensional biodiversity hotspots and the future of taxonomic, ecological, and phylogenetic diversity: a case study of North American rodents

Tara Smiley, Pascal Title, Miriam Zelditch & Rebecca Terry
Aim: We investigate geographic patterns across taxonomic, ecological, and phylogenetic diversity to test for spatial (in)congruency and identify aggregate diversity hotspots in relation to present land-use and future climate. Simulating extinctions of imperiled species, we demonstrate where losses across diversity dimensions and geography are predicted. Location: North America Time period: Present-day, future Major taxa studied: Rodentia Methods: Using geographic range maps for rodent species, we quantified spatial patterns for eleven dimensions of diversity: taxonomic (species,...

Rapid reversal of a potentially constraining genetic covariance between leaf and flower traits in Silene latifolia

Janet Steven, Ingrid Anderson, Edmund Brodie & Lynda Delph
Genetic covariance between two traits generates correlated responses to selection, and may either enhance or constrain adaptation. Silene latifolia exhibits potentially constraining genetic covariance between specific leaf area and flower number in males. Flower number is likely to increase via fecundity selection but the correlated increase in specific leaf area increases mortality, and specific leaf area is under selection to decrease in dry habitats. We selected on trait combinations in two selection lines for four...

A Bayesian extension of phylogenetic generalized least squares (PGLS): incorporating uncertainty in the comparative study of trait relationships and evolutionary rates

Jesualdo Arturo Fuentes González, P. David Polly & Emília P. Martins
Phylogenetic comparative methods use tree topology, branch lengths, and models of phenotypic change to take into account non-independence in statistical analysis. However, these methods normally assume that trees and models are known without error. Approaches relying on evolutionary regimes also assume specific distributions of character states across a tree, which often result from ancestral state reconstructions that are subject to uncertainty. Several methods have been proposed to deal with some of these sources of uncertainty,...

Intraspecific mating system evolution and its effect on complex male secondary sexual traits: does male-male competition increase selection on size or shape?

Julian Baur, Jeannine Roy, Martin A. Schäfer, Nalini Puniamoorthy, Wolf U. Blanckenhorn & Patrick T. Rohner
Sexual selection is generally held responsible for the exceptional diversity in secondary sexual traits in animals. Mating system evolution is therefore expected to profoundly affect the covariation between secondary sexual traits and mating success. While there is such evidence at the interspecific level, data within species remain scarce. We here investigate sexual selection acting on the exaggerated male fore femur and the male wing in the common and widespread dung flies Sepsis punctum and S....

Genotypic variation in parasite avoidance behavior and other mechanistic, non-linear components of transmission

Alexander Strauss
Traditional epidemiological models assume that transmission increases proportionally to the density of parasites. However, empirical data frequently contradict this assumption. General yet mechanistic models can explain why transmission depends non-linearly on parasite density and thereby identify potential defensive strategies of hosts. For example, hosts could decrease their exposure rates at higher parasite densities (via behavioral avoidance) or decrease their per-parasite susceptibility when encountering more parasites (e.g., via stronger immune responses). To illustrate, we fit mechanistic...

Data from: Desiccation resistance and pigmentation variation reflects bioclimatic differences in the Drosophila americana species complex

Jeremy S Davis & Leonie Moyle
Background: Disentangling the selective factors shaping adaptive trait variation is an important but challenging task. Many studies—especially in Drosophila—have documented trait variation along latitudinal or altitudinal clines, but frequently lack resolution about specific environmental gradients that could be causal selective agents, and often do not investigate covariation between traits simultaneously. Here we examined variation in multiple macroecological factors across geographic space and their associations with variation in three physiological traits (desiccation resistance, UV resistance, and...

Data from: City sicker? a meta-analysis of wildlife health and urbanization

Maureen H. Murray, Cecilia A. Sanchez, Daniel J. Becker, Kaylee A. Byers, Katherine E. L. Worsley-Tonks & Meggan E. Craft
Urban development can alter resource availability, land use, and community composition, in turn influencing wildlife health. Generalizable relationships between wildlife health and urbanization have yet to be quantified, and could vary across health metrics and animal taxonomy. We present a phylogenetic meta-analysis of 516 records spanning 81 wildlife species from 106 studies comparing the toxicant loads, parasitism, body condition, or stress of urban and non-urban wildlife populations in 30 countries. We find a significantly negative...

Data from: Serotonin differentially affects morph-specific behavior in divergent populations of a horned beetle

Keeley D. Newsom, Armin P. Moczek & Daniel B. Schwab
Associations between animal weapons and corresponding aggressive behaviors are among the most characteristic features of species, yet at the same time their co-expression is itself often strongly dependent on context, such as male condition or population ecology. Yet the mechanisms that modulate associations between aggression, morphology, and biological context remain poorly understood. The biogenic amine serotonin has been shown to regulate a wide range of aggressive and morph-specific behaviors in diverse insect species. However, the...

Data from: Similarity in temporal variation in sex-biased dispersal over short and long distances in the dark-eyed junco, Junco hyemalis

Eric B. Liebgold, Nicole M. Gerlach & Ellen D. Ketterson
Patterns of sex-biased dispersal are typically consistent within taxa, e.g., female-biased in birds and male-biased in mammals, leading to theories about the evolutionary pressures that lead to sex-biased dispersal. However, generalizations about the evolution of sex biases tend to overlook that dispersal is mediated by ecological factors that vary over time. We examined potential temporal variation in between- and within-population dispersal over an 11-year period in a bird, the dark-eyed junco (Junco hyemalis). We measured...

Data from: Inferring the history of interchromosomal gene transposition in Drosophila using n-Dimensional parsimony

Mira V. Han & Matthew W. Hahn
Gene transposition puts a new gene copy in a novel genomic environment. Moreover, genes moving between the autosomes and the X chromosome experience change in several evolutionary parameters. Previous studies of gene transposition have not utilized the phylogenetic framework that becomes possible with the availability of whole genomes from multiple species. Here we used parsimonious reconstruction on the genomic distribution of gene families to analyze interchromosomal gene transposition in Drosophila. We identified 782 genes that...

Data from: Impact of genetic reduction of NMNAT2 on chemotherapy-induced losses in cell viability in vitro and peripheral neuropathy in vivo

Richard A. Slivicki, Yousuf O. Ali, Hui-Chen Lu & Andrea G. Hohmann
Nicotinamide mononucleotide adenylyl transferases (NMNATs) are essential neuronal maintenance factors postulated to preserve neuronal function and protect against axonal degeneration in various neurodegenerative disease states. We used in vitro and in vivo approaches to assess the impact of NMNAT2 reduction on cellular and physiological functions induced by treatment with a vinca alkaloid (vincristine) and a taxane-based (paclitaxel) chemotherapeutic agent. NMNAT2 null (NMNAT2-/-) mutant mice die at birth and cannot be used to probe functions of...

Data from: Detection and polarization of introgression in a five-taxon phylogeny

James B. Pease & Matthew W. Hahn
When multiple speciation events occur rapidly in succession, discordant genealogies due to incomplete lineage sorting (ILS) can complicate the detection of introgression. A variety of methods, including the D-statistic (a.k.a. the “ABBA–BABA test”), have been proposed to infer introgression in the presence of ILS for a four-taxon clade. However, no integrated method exists to detect introgression using allelic patterns for more complex phylogenies. Here we explore the issues associated with previous systems of applying D-statistics...

Data from: Spatial soil heterogeneity has a greater effect on symbiotic arbuscular mycorrhizal fungal communities and plant growth than genetic modification with Bacillus thuringiensis toxin genes

Tanya E. Cheeke, Ursel M. Schütte, Chris M. Hemmerich, Mitchell B. Cruzan, Todd N. Rosenstiel & James D. Bever
Maize, genetically modified with the insect toxin genes of Bacillus thuringiensis (Bt), is widely cultivated, yet its impacts on soil organisms are poorly understood. Arbuscular mycorrhizal fungi (AMF) form symbiotic associations with plant roots and may be uniquely sensitive to genetic changes within a plant host. In this field study, the effects of nine different lines of Bt maize and their corresponding non-Bt parental isolines were evaluated on AMF colonization and community diversity in plant...

Data from: Reanalysis suggests that genomic islands of speciation are due to reduced diversity, not reduced gene flow

Tami E. Cruickshank & Matthew W. Hahn
The metaphor of “genomic islands of speciation” was first used to describe heterogeneous differentiation among loci between the genomes of closely related species. The biological model proposed to explain these differences was that the regions showing high levels of differentiation were resistant to gene flow between species, while the remainder of the genome was being homogenized by gene flow and consequently showed lower levels of differentiation. However, the conditions under which such differentiation can occur...

Data from: Genome skimming reveals the origin of the Jerusalem Artichoke tuber crop species: neither from Jerusalem nor an Artichoke

Dan G. Bock, Nolan C. Kane, Daniel P. Ebert & Loren H. Rieseberg
The perennial sunflower Helianthus tuberosus, known as Jerusalem Artichoke or Sunchoke, was cultivated in eastern North America before European contact. As such, it represents one of the few taxa that can support an independent origin of domestication in this region. Its tubers were adopted as a source of food and forage when the species was transferred to the Old World in the early 1600s, and are still used today. Despite the cultural and economic importance...

Data from: Localized hotspots drive continental geography of abnormal amphibians on U.S. wildlife refuges

Mari K. Reeves, Kimberly A. Medley, Alfred E. Pinkney, Marcel Holyoak, Pieter T. J. Johnson & Michael J. Lannoo
Amphibians with missing, misshapen, and extra limbs have garnered public and scientific attention for two decades, yet the extent of the phenomenon remains poorly understood. Despite progress in identifying the causes of abnormalities in some regions, a lack of knowledge about their broader spatial distribution and temporal dynamics has hindered efforts to understand their implications for amphibian population declines and environmental quality. To address this data gap, we conducted a nationwide, 10-year assessment of 62,947...

Data from: The population genomics of sunflowers and genomic determinants of protein evolution revealed by RNAseq

Sébastien Renaut, Christopher J. Grassa, Brook T. Moyers, Nolan C. Kane, Loren H. Rieseberg, Christopher Grassa, Brook Moyers, Nolan Kane & Loren Rieseberg
Few studies have investigated the causes of evolutionary rate variation among plant nuclear genes, especially in recently diverged species still capable of hybridizing in the wild. The recent advent of Next Generation Sequencing (NGS) permits investigation of genome wide rates of protein evolution and the role of selection in generating and maintaining divergence. Here, we use individual whole-transcriptome sequencing (RNAseq) to refine our understanding of the population genomics of a wild species of sunflowers (Helianthus...

Data from: Patterns of transposable element variation and clinality in Drosophila

Jeffrey R. Adrion, David J. Begun & Matthew W. Hahn
Natural populations often exist in spatially diverse environments and may experience variation in the strength and targets of natural selection across their ranges. Drosophila provides an excellent opportunity to study the effects of spatially varying selection in natural populations, as both D. melanogaster and D. simulans live across a wide range of environments in North America. Here, we characterize patterns of variation in transposable elements (TEs) from six populations of D. melanogaster and nine populations...

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