217 Works

Data from: Patterns of domestication in the Ethiopian oil-seed crop Noug (Guizotia abyssinica)

Hannes Dempewolf, Misteru Tesfaye, Abel Teshome, Anne Bjorkman, Rose L. Andrew, Moira Scascitelli, Scott Black, Endashaw Bekele, Johannes M. M. Engels, Quentin C. B. Cronk, Loren H. Rieseberg & Anne D. Bjorkman
Noug (Guizotia abyssinica) is a semi-domesticated oil-seed crop, which is primarily cultivated in Ethiopia. Unlike its closest crop relative, sunflower, noug has small seeds, small flowering heads, many branches, many flowering heads, indeterminate flowering, and it shatters in the field. Here we conducted common garden studies and microsatellite analyses of genetic variation to test whether high levels of crop-wild gene flow and/or unfavorable phenotypic correlations have hindered noug domestication. With the exception of one population,...

Data from: An experimental test of the relationship between yolk testosterone and the social environment in a colonial passerine

Alexandra B. Bentz, Victoria A. Andreasen & Kristen J. Navara
Maternal hormones can be transferred to offspring during prenatal development in response to the maternal social environment, and may adaptively alter offspring phenotype. For example, numerous avian studies show that aggressive competition with conspecifics tends to result in females allocating more testosterone to their egg yolks, and this may cause offspring to have more competitive phenotypes. However, deviations from this pattern of maternal testosterone allocation are found, largely in studies of colonial species, and have...

Data from: \"Development of the draft genome sequence of the marbled flounder Pseudopleuronectes yokohamae as a reference of population genomic analysis\" in Genomic Resources Notes accepted 1 February 2015 – 31 March 2015

Yuki Minegishi, Minoru Ikeda, Lynda F. Delph, Laura A. Weingartner, Peter D. Fields, Laura Bertini, Carla Caruso, Silvia Proietti, Wolfgang Arthofer, Francesco Cicconardi, Heike Ritthammer, Birgit C. Schlick-Steiner, Florian M. Steiner, Gregor A. Wachter & Herbert C. Wagner
This article documents the public availability of the draft genome sequence data (raw reads, assembled contigs and unassembled reads) and RAD-tag read data of the marbled flounder Pseudopleuronectes yokohamae (Pleuronectiformes; Pleuronectidae).

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...

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: 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...

Don’t stand so close to me: microbiota-facilitated enemy release dynamics in introduced Onthophagus taurus dung beetles.

Erik Parker
Microbial symbionts can influence their hosts in stunningly diverse ways. Emerging research suggests that an underappreciated facet of these relationships is the influence microbes can have on their host’s responses to novel, or stressful, environmental conditions. We sought to address these and related questions in populations resulting from the recent introduction and subsequent rapid range expansion of Onthophagus taurus dung beetles. Specifically, we manipulated both microbial communities and rearing temperature to detect signatures of developmental...

Local adaptation from afar: migratory bird populations diverge in the initiation of reproductive timing while wintering in sympatry

Sarah Wanamaker, Devraj Singh, Allison Byrd, Tara Smiley & Ellen Ketterson
The initiation of reproduction in many seasonally breeding animals is controlled by photoperiod and tends to be clinal: populations at higher latitudes breed later than those at lower latitudes, often reflecting a higher photoperiodic threshold. Migratory animals presumably time reproduction to match conditions at their breeding grounds at least in part by cues perceived on their wintering grounds. We asked how closely related dark-eyed junco (Junco hyemalis) populations that overwinter in sympatry but breed in...

Data from: Virulent disease epidemics can increase host density by depressing foraging of hosts

Rachel Penczykowski, Marta Shocket, Jessica Housley Ochs, Brian Lemanski, Hema Sundar, Meghan Duffy & Spencer Hall
All else equal, parasites that harm host fitness should depress densities of their hosts. However, parasites that alter host traits may increase host density via indirect ecological interactions. Here, we show how depression of foraging rate of infected hosts can produce such a hydra effect. Using a foraging assay, we quantified reduced foraging rates of a zooplankton host infected with a virulent fungal parasite. We then parameterized a dynamical model of hosts, parasites, and resources...

Data from: \"Transcriptome resources for two highly divergent Silene latifolia populations\" in Genomic Resources Notes accepted 1 February 2015 – 31 March 2015

Peter Fields, Laura Weingartner & Lynda Delph
Here we have used next-generation Illumina sequencing to generate transcriptomes of four S. latifolia individuals from two morphologically divergent populations from disparate habitats, including including two females from Xativa, Spain and two males from Zagreb, Croatia. Spanish plants experience a much hotter, drier climate than Croatian plants, and the populations have ecologically relevant differences in floral and leaf characteristics (e.g., Spain has thicker leaves and produces fewer, larger flowers in comparison) (data not shown). This...

Data from: Genome scans reveal candidate domestication and improvement genes in cultivated sunflower, as well as post-domestication introgression with wild relatives.

Gregory J. Baute, Nolan C. Kane, Christopher J. Grassa, Zhao Lai & Loren H. Rieseberg
• The development of modern crops typically involves both selection and hybridization, but to date most studies have focused on the former. In the present study we explore how both processes, and their interactions, have molded the genome of the cultivated sunflower, a globally important oilseed. • To identify genes targeted by selection during the domestication and improvement of sunflower, and to detect post-domestication hybridization with wild species, we analyzed transcriptome sequences of 80 genotypes,...

Data from: A quantitative proteomic analysis of cofilin phosphorylation in myeloid cells and its modulation using the LIM kinase inhibitor Pyr1

Renaud Prudent, Nathalie Demoncheaux, Hélène Diemer, Véronique Collin-Faure, Reuben Kapur, Fabrice Paublant, Laurence Lafanechère, Sarah Cianférani & Thierry Rabilloud
LIM kinases are located at a strategic crossroad, downstream of several signaling pathways and upstream of effectors such as microtubules and the actin cytoskeleton. Cofilin is the only LIM kinases substrate that is well described to date, and its phosphorylation on serine 3 by LIM kinases controls cofilin actin-severing activity. Consequently, LIM kinases inhibition leads to actin cytoskeleton disorganization and blockade of cell motility, which makes this strategy attractive in anticancer treatments. LIMK has also...

Data from: The timing of molecular and morphological changes underlying reproductive transitions in wild tomatoes (Solanum sect. Lycopersicon)

Stacey L. Vosters, Cathleen P. Jewell, Natasha A. Sherman, Frances Einterz, Benjamin K. Blackman & Leonie C. Moyle
Molecular mechanisms underlying the transition from genetic self-incompatibility to self-compatibility are well documented, but the evolution of other reproductive trait changes that accompany shifts in reproductive strategy (mating system) remain comparatively poorly understood. A notable exception is the transition from exserted styles to styles with recessed positions relative to the anthers in wild tomatoes (Solanum Section Lycopersicon). This phenotypic change has been previously attributed to specific mutation in the promoter of a gene that influences...

Data from: Signals of selection in conditionally expressed genes in the diversification of three horned beetles species

Melissa H. Pespeni, Jason T. Ladner & Armin P. Moczek
Species radiations may be facilitated by phenotypic differentiation already present within populations, such as those arising through sex-specific development or developmental processes biased toward particular reproductive or trophic morphs. We sought to test this hypothesis by utilizing a comparative transcriptomic approach to contrast among and within-species differentiation using three horned beetle species in the genus Onthophagus. These three species exhibit differences along three phenotypic axes reflective of much of the interspecific diversity present within the...

Data from: Multiple reproductive barriers separate recently diverged sunflower ecotypes

Katherine L. Ostevik, Rose L. Andrew, Sarah P. Otto & Loren H. Rieseberg
Measuring reproductive barriers between groups of organisms is an effective way to determine the traits and mechanisms that impede gene flow. However, to understand the ecological and evolutionary factors that drive speciation, it is important to distinguish between the barriers that arise early in the speciation process and those that arise after speciation is largely complete. In this paper we comprehensively test for reproductive isolation between recently diverged (< 10,000 years bp) dune and non-dune...

Data from: Specialization of a polyphenism switch gene following serial duplications in Pristionchus nematodes

Erik J. Ragsdale & Nicholas A. Ivers
Polyphenism is an extreme manifestation of developmental plasticity, requiring distinct developmental programs and the addition of a switch mechanism. Because the genetic basis of polyphenism switches has only begun to be understood, how their mechanisms arise is unclear. In the nematode Pristionchus pacificus, which has a mouthpart polyphenism specialized for alternative diets, a gene (eud-1) executing the polyphenism switch was recently identified as the product of lineage-specific duplications. Here, we infer the role of gene...

Data from: MycoDB, a global database of plant response to mycorrhizal fungi

V. Bala Chaudhary, Megan A. Rúa, Anita Antoninka, James D. Bever, Jeffery Cannon, Ashley Craig, Jessica Duchicela, Alicia Frame, Monique Gardes, Catherine Gehring, Michelle Ha, Miranda Hart, Jacob Hopkins, Baoming Ji, Nancy Collins Johnson, Wittaya Kaonongbua, Justine Karst, Roger T. Koide, Louis J. Lamit, James Meadow, Brook G. Milligan, John C. Moore, , Bridget Piculell, Blake Ramsby … & Jason D. Hoeksema
Plants form belowground associations with mycorrhizal fungi in one of the most common symbioses on Earth. However, few large-scale generalizations exist for the structure and function of mycorrhizal symbioses, as the nature of this relationship varies from mutualistic to parasitic and is largely context-dependent. We announce the public release of MycoDB, a database of 4,010 studies (from 438 unique publications) to aid in multi-factor meta-analyses elucidating the ecological and evolutionary context in which mycorrhizal fungi...

Data from: \"A reduced representation libraries approach for nuclear marker development via 454 sequencing applied on Tetramorium (Hymenoptera: Formicidae)\" in Genomic Resources Notes Accepted 1 February 2015 to 31 March 2015

Herbert C. Wagner, Francesco Cicconardi, Gregor A. Wachter, Heike Ritthammer, Florian M. Steiner, Birgit C. Schlick-Steiner & Wolfgang Arthofer
To clarify species boundaries in the cryptic Tetramorium caespitum/impurum ant species complex, a multi-disciplinary approach is necessary. Nuclear DNA markers constitute one important step in species delimitation. We established a reduced representation library (RRL) based on amplified fragment-length polymorphism (AFLP) PCR products of four species. Amplicons were size-selected by gel-electrophoresis, DNA-fragments recovered from the agarose gels, and 454 libraries constructed by a commercial provider. Pyrosequencing yielded 490,155 reads, from which we designed cross-species amplifying primer...

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: Why concatenation fails near the anomaly zone

Fabio K. Mendes & Matthew W. Hahn
Genome-scale sequencing has been of great benefit in recovering species trees, but has not provided final answers. Despite the rapid accumulation of molecular sequences, resolving short and deep branches of the tree of life has remained a challenge, and has prompted the development of new strategies that can make the best use of available data. One such strategy – the concatenation of gene alignments – can be successful when coupled with many tree estimation methods,...

Data from: Evaluating shell variation across different populations of a freshwater snail

Daniela Vergara, Jesualdo A. Fuentes, Kayla S. Stoy & Curtis M. Lively
The freshwater snail Potamopyrgus antipodarum has become a model system for studying invasion ecology, host–parasite coevolution, the maintenance of sexual reproduction and ecotoxicology. One understudied aspect of this snail is the variation in morphology within and among populations, which could provide insights into ecological differences across its native range. In this study of 17 New Zealand lake populations of P. antipodarum we used linear measurements and geometric morphometrics to compare several aspects of shell size...

Data from: Oxidative stress-mediated NFκB phosphorylation upregulates p62/SQSTM1 and promotes retinal pigmented epithelial cell survival through increased autophagy

Chunjuan Song, Sayak K. Mitter, Xiaoping Qi, Eleni Beli, Haripriya V. Rao, Jindong Ding, Colin S. Ip, Hongmei Gu, Debra Akin, William A. Dunn, Catherine Bowes Rickman, Alfred S. Lewin, Maria B. Grant & Michael E. Boulton
p62 is a scaffolding adaptor implicated in the clearance of protein aggregates by autophagy. Reactive oxygen species (ROS) can either stimulate or inhibit NFκB-mediated gene expression influencing cellular fate. We studied the effect of hydrogen peroxide (H2O2)-mediated oxidative stress and NFκB signaling on p62 expression in the retinal pigment epithelium (RPE) and investigated its role in regulation of autophagy and RPE survival against oxidative damage. Cultured human RPE cell line ARPE-19 and primary human adult...

Data from: Specialization of a polyphenism switch gene following serial duplications in Pristionchus nematodes

Erik J. Ragsdale & Nicholas A. Ivers
Polyphenism is an extreme manifestation of developmental plasticity, requiring distinct developmental programs and the addition of a switch mechanism. Because the genetic basis of polyphenism switches has only begun to be understood, how their mechanisms arise is unclear. In the nematode Pristionchus pacificus, which has a mouthpart polyphenism specialized for alternative diets, a gene (eud-1) executing the polyphenism switch was recently identified as the product of lineage-specific duplications. Here, we infer the role of gene...

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...

Data from: Predatory lizards perceive plant-derived volatile odorants

Jay K. Goldberg, Genevieve Pintel, Stacey L. Weiss & Emilia P. Martins
Many lizards are olfactory foragers and prey upon herbivorous arthropods, yet their responses to common herbivore‐associated plant volatiles remain unknown. As such, their role in mediating plant indirect defenses also remains largely obscured. In this paper, we use a cotton‐swab odor presentation assay to ask whether lizards respond to two arthropod‐associated plant‐derived volatile compounds: 2‐(E)‐hexenal and hexanoic acid. We studied the response of two lizard species, Sceloporus virgatusand Aspidoscelis exsanguis, because they differ substantially in...

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