277 Works

Fire emissions data before and after peatland restoration, Indonesia, 2004-2015

L. Kiely, D.V. Spracklen & C. Wiedinmyer
This dataset contains fire emissions from Equatorial Asia for the years 2004, 2006, 2009, 2012, 2014 and 2015. The data is based on the Fire Inventory from National Center for Atmospheric Research with the addition of emissions from Indonesian peat fires, which contribute substantially to fire emissions in the region. The files for each year contain daily information on the area burned and emissions of several species, including CO, CO2 and PM2.5. Data is given...

Data from: Population genomics of natural and experimental populations of guppies (Poecilia reticulata)

Bonnie A. Fraser, Axel Künstner, David N. Reznick, Christine Dreyer & Detlef Weigel
Convergent evolution represents one of the best lines of evidence for adaptation, but few cases of phenotypic convergence are understood at the genetic level. Guppies inhabiting the Northern Mountain Range of Trinidad provide a classic example of phenotypic convergent evolution, where adaptation to low or high predation environments has been found for a variety of traits. A major advantage of this system is the possibility of long-term experimental studies in nature, including transplantation from high...

Data from: Predicting the response to simultaneous selection: genetic architecture and physiological constraints

Goggy Davidowitz, H. Frederik Nijhout & Derek A. Roff
A great deal is known about the evolutionary significance of body size and development time. They are determined by the non-linear interaction of three physiological traits: two hormonal events and growth rate. In this study we investigate how the genetic architecture of the underlying three physiological traits affects the simultaneous response to selection on the two life history traits in the hawk moth Manduca sexta. The genetic architecture suggests that when the two life history...

Data from: Ecological and phylogenetic variability in the spinalis muscle of snakes

Jessica L. Tingle, Gabriel E.A. Gartner, Bruce C. Jayne, , G. E. A. Gartner & T. Garland
Understanding the origin and maintenance of functionally important subordinate traits is a major goal of evolutionary physiologists and ecomorphologists. Within the confines of a limbless body plan, snakes are diverse in terms of body size and ecology, but we know little about the functional traits that underlie this diversity. We used a phylogenetically diverse group of 131 snake species to examine associations between habitat use, sidewinding locomotion, and constriction behavior with the number of body...

Data from: Replicated origin of female biased adult sex ratio in introduced populations of the Trinidadian guppy (Poecilia reticulata).

Jeffrey D. Arendt, David N. Reznick & Andres López-Sepulcre
There are many theoretical and empirical studies explaining variation in offspring sex ratio but relatively few that explain variation in adult sex ratio. Adult sex ratios are important because biased sex ratios can be a driver of sexual selection and will reduce effective population size which affects population persistence and shapes how populations respond to natural selection. Previous work on guppies (Poecilia reticulata) gives mixed results, usually showing a female-biased adult sex ratio. However a...

Data from: Pathogen shifts in a honey bee predator following arrival of the Varroa mite

Kevin J. Loope, James W. Baty, Phil J. Lester & Erin E. Wilson Rankin
Emerging infectious diseases (EIDs) are a global threat to honey bees, and spillover from managed bees threaten wider insect populations. Deformed wing virus (DWV), a widespread virus that has become emergent in conjunction with the spread of the mite Varroa destructor, is thought to be partly responsible for global colony losses. The arrival of Varroa in honey bee populations causes a dramatic loss of viral genotypic diversity, favoring a few virulent strains. Here, we investigate...

Data from: The phenotypic correlates and quantitative genetics of masculinization in the rodent, Octodon degus

Derek A. Roff, Matthew E. Wolak, Loreto A. Correa & Mauricio Soto-Gamboa
In some mammals female characteristics have been shown to depend in part on the intrauterine position during development of female fetuses relative to male fetuses. Females developing in close proximity to males show behavioural, physiological and life history characteristics that are masculinized. With the exception of one inconclusive study, nothing is known of the genetic basis of this phenomenon. In this paper we reported an analysis of the quantitative genetic basis of masculinization, as indicated...

Data from: A test of the hypothesis that correlational selection generates genetic correlations

Derek A. Roff & Daphne J. Fairbairn
Theory predicts that correlational selection on two traits will cause the major axis of the bivariate G matrix to orient itself in the same direction as the correlational selection gradient. Two testable predictions follow from this: for a given pair of traits (1) the sign of correlational selection gradient should be the same as that of the genetic correlation, and (2) the correlational selection gradient should be positively correlated with the value of the genetic...

Data from: Diversity-dependent evolutionary rates in early Paleozoic zooplankton

Michael Foote, Roger A. Cooper, James S. Crampton & Peter M. Sadler
The extent to which biological diversity affects rates of diversification is central to understanding macroevolutionary dynamics, yet no consensus has emerged on the importance of diversity-dependence of evolutionary rates. Here we analyse the species-level fossil record of early Paleozoic graptoloids, documented with high temporal resolution, to test directly whether rates of diversification were influenced by levels of standing diversity within this major clade of marine zooplankton. To circumvent the statistical regression-to-the-mean artefact, whereby higher- and...

Data from: Analysis of expressed sequence tags from the placenta of the live-bearing fish Poeciliopsis (Poeciliidae)

Tamara M Panhuis, Gina Broitman-Maduro, Jarrod Uhrig, Morris Maduro & David N Reznick
Matrotrophic fish in the genus Poeciliopsis (Poeciliidae) have a placenta-like structure used in post-fertilization maternal provisioning of the developing embryo. To understand better the structure and function of the Poeciliopsis placenta we derived cDNA libraries from the maternal follicular placenta of two matrotrophic Poeciliopsis sister species, P. turneri and P. presidionis. These species inherited their placenta from a common ancestor and represent one of three independent origins of placentas in Poeciliopsis. Expressed sequence tags were...

Data from: Predation-associated differences in sex-linkage of wild guppy coloration

Swanne Pamela Gordon, Andrés López-Sepulcre & David N Reznick
Evolutionary theory predicts that the sex-linkage of sexually selected traits can influence the direction and rate of evolutionary change, and also itself be subject to selection. Theory abounds on how sex-specific selection, mate choice, or other phenomena should favor different types of sex-linked inheritance, yet evidence in nature remains limited. Here we use hormone assays in Trinidadian guppies to explore the extent to which linkage of male coloration differs among populations adapted to varying predation...

Data from: Post-fire recovery in coastal sage scrub: seed rain and community trajectory

Erin Conlisk, Rebecca Swab, Alejandra Martínez-Berdeja & Matthew P. Daugherty
Disturbance is a primary mechanism structuring ecological communities. However, human activity has the potential to alter the frequency and intensity of natural disturbance regimes, with subsequent effects on ecosystem processes. In Southern California, human development has led to increased fire frequency close to urban areas that can form a positive feedback with invasive plant spread. Understanding how abiotic and biotic factors structure post-fire plant communities is a critical component of post-fire management and restoration. In...

Data from: Organization of biogeochemical nitrogen pathways with switch-like adjustment in fluctuating soil redox conditions

Sanjay Lamba, Soumen Bera, Mubasher Rashid, Alexander B. Medvinsky, Gui-Quan Sun, Claudia Acquisti, Amit Chakraborty & Bai-Lian Li
Nitrogen is cycled throughout ecosystems by a suite of biogeochemical processes. The high complexity of the nitrogen cycle resides in an intricate interplay between reversible biochemical pathways alternatively and specifically activated in response to diverse environmental cues. Despite aggressive research, how the fundamental nitrogen biochemical processes are assembled and maintained in fluctuating soil redox conditions remains elusive. Here, we address this question using a kinetic modelling approach coupled with dynamical systems theory and microbial genomics....

#Blackwomanhood

Bergis Jules
The #blackwomanhood Twitter chat took place on May 10th, 2018. It was a discussion around the syllabus for the Black Womanhood course taught by Martha Jones and Jessica Marie Johnson at Johns Hopkins University. http://dh.jmjafrx.com/2018/01/27/black-womanhood-the-syllabus/

I Voted For Trump

Bergis Jules
The phrase "I Voted For Trump" began trending on Twitter on August, 17th, 2017. It includes tweets from supporters and opponents of President Donald Trump. This collection contains 140,000 tweet ids. The tweet ids were collected using the DocNow tweet collection prototype tool: http://app.docnow.io/ The tweet ids can be turned back into the original tweets using the DocNow tweet hydration tool: https://github.com/docnow/hydrator#readme

Data from: Cascading effects of mammalian herbivores on ground-dwelling arthropods: variable responses across arthropod groups, habitats and years

Eric M. Cecil, Marko J. Spasojevic & J. Hall Cushman
1. Large mammalian herbivores are well known to shape the structure and function of ecosystems worldwide and these effects can in turn cascade through systems to indirectly influence other animal species. A wealth of studies have explored the effects of large mammals on arthropods, but to date they have reported such widely varying results that generalizations have been elusive. Three factors are likely drivers of this variability: the widely varying life-history characteristics of different arthropod...

Data from: Early consequences of allopolyploidy alter floral evolution in Nicotiana (Solanaceae)

Elizabeth W. McCarthy, Jacob B. Landis, Amelda Kurti, Amber J. Lawhorn, Mark W. Chase, Sandra Knapp, Steven C. Le Comber, Andrew R. Leitch & Amy Litt
Background: Polyploidy has played a major role in angiosperm evolution. Previous studies have examined polyploid phenotypes in comparison to their extant progenitors, but not in context of predicted progenitor phenotypes at allopolyploid origin. In addition, differences in the trends of polyploid versus diploid evolution have not been investigated. We use ancestral character-state reconstructions to estimate progenitor phenotype at allopolyploid origin to determine patterns of polyploid evolution leading to morphology of the extant species. We also...

Data from: Crossing the uncrossable: novel trans-valley biogeographic patterns revealed in the genetic history of low dispersal mygalomorph spiders (Antrodiaetidae, Antrodiaetus) from California

Marshal Hedin, James Starrett & Cheryl Hayashi
Antrodiaetus riversi is a dispersal-limited, habitat specialized mygalomorph spider species endemic to mesic woodlands of northern and central California. Here we build upon prior phylogeographic research using a much larger geographic sample and include additional nuclear genes, providing more detailed biogeographic insights throughout the range of this complex. Of particular interest is the uncovering of unexpected and replicated trans-valley biogeographic patterns, where in two separate genetic clades western haplotypes in the California south Coast Ranges...

Data from: Convergent evolution of alternative developmental trajectories associated with diapause in African and South American killifish

Andrew I. Furness, David N. Reznick, Mark S. Springer & Robert W. Meredith
Annual killifish adapted to life in seasonally ephemeral water-bodies exhibit desiccation resistant eggs that can undergo diapause, a period of developmental arrest, enabling them to traverse the otherwise inhospitable dry season. Environmental cues that potentially indicate the season can govern whether eggs enter a stage of diapause mid-way through development or skip this diapause and instead undergo direct development. We report, based on construction of a supermatrix phylogenetic tree of the order Cyprinodontiformes and a...

An ancient and eroded social supergene is widespread across Formica ants

Alan Brelsford, Jessica Purcell, Amaury Avril, Patrick Tran Van, Junxia Zhang, Timothée Brütsch, Liselotte Sundström, Heikki Helanterä & Michel Chapuisat
Supergenes, clusters of tightly linked genes, play a key role in the evolution of complex adaptive variation. While supergenes have been identified in many species, we lack an understanding of their origin, evolution and persistence. Here, we uncover 20-40 MY of evolutionary history of a supergene associated with polymorphic social organization in Formica ants. We show that five Formica species exhibit homologous divergent haplotypes spanning 11 Mbp on chromosome 3. Despite the size of the...

Data for differential feeding responses of several bee species to sugar sources containing Iridomyrmecin, an Argentine ant trail pheromone component

Erin Wilson Rankin, Jacob Cecala, Dong-Hwan Choe & Nohely Hernandez Pineda
These data describe the bioassays associated with published article, doi: 10.1007/s10905-020-09748-8 (Differential Feeding Responses of Several Bee Species to Sugar Sources Containing Iridomyrmecin, an Argentine Ant Trail Pheromone Component). We investigated the response of three commercially important pollinator species to a pheromone deposited by Argentine ants at a food source. The Argentine ant Linepithema humile is one of the most invasive and problematic ant species; it has been introduced to Mediterranean-type habitats around the globe....

Development of the early Cambrian oryctocephalid trilobite Oryctocarella duyunensis from western Hunan, China

Tao Dai, Nigel Hughes, Xingliang Zhang & Shanchi Peng
Abundant articulated specimens of the oryctocarine trilobite Oryctocarella duyunensis from the lower Cambrian (Stage 4, Series 2) Balang Formation at the Bulin section in western Hunan Province, South China, permit the description of all meraspid degrees. The maximum number of thoracic segments observed in this collection is 11. Meraspid growth was accompanied by progressive and gradual change in overall form, and this animal showed an homonomously segmented trunk with variation in the number of pygidial...

Data from: Rapid evolution and plasticity of genitalia

E. Dale Broder, Cameron K. Ghalambor, Corey A. Handelsman, Emily W. Ruell, David N. Reznick & Lisa M. Angeloni
Genital morphology exhibits tremendous variation and is intimately linked with fitness. Sexual selection, nonmating natural selection, and neutral forces have been explored as potential drivers of genital divergence. Though less explored, genitalia may also be plastic in response to the developmental environment. In poeciliid fishes, the length of the male intromittent organ, the gonopodium, may be driven by sexual selection if longer gonopodia attract females or aid in forced copulation attempts, or by nonmating natural...

Ediacara growing pains: Modular addition and development in Dickinsonia costata

Scott Evans, James G. Gehling, Douglas Erwin & Mary Droser
Constraining patterns of growth using directly observable and quantifiable characteristics can reveal a wealth of information regarding the biology of the Ediacara Biota – the oldest macroscopic, complex community forming organisms in the fossil record. However, these rely on individuals captured at an instant in time at various growth stages, and so different interpretations can be derived from the same material. Here we leverage newly discovered and well-preserved Dickinsonia costata Sprigg 1947 from South Australia,...

Data for: Theoretical and practical considerations when using retroelement insertions to estimate species trees in the anomaly zone

Erin Molloy, John Gatesy & Mark Springer
A potential shortcoming of concatenation methods for species tree estimation is their failure to account for incomplete lineage sorting. Coalescent methods address this problem but make various assumptions that, if violated, can result in worse performance than concatenation. Given the challenges of analyzing DNA sequences with both concatenation and coalescent methods, retroelement insertions (RIs) have emerged as powerful phylogenomic markers for species tree estimation. Here, we show that two recently proposed quartet-based methods, SDPquartets and...

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