94 Works

Data from: The population structure and recent colonization history of Oregon threespine stickleback determined using restriction-site associated DNA-sequencing

Julian Catchen, Susan Bassham, Taylor Wilson, Mark Currey, Conor O'Brien, Quick Yeates & William A. Cresko
Understanding how genetic variation is partitioned across genomes within and among populations is a fundamental problem in ecological and evolutionary genetics. To address this problem, we studied the threespine stickleback fish, which has repeatedly undergone parallel phenotypic and genetic differentiation when oceanic fish have invaded freshwater habitats. While significant evolutionary genetic research has been performed using stickleback from geographic regions that have been deglaciated in the last 20 000 years, less research has focused on...

Data from: Association between integration structure and functional evolution in the opercular four-bar apparatus of the threespine stickleback, Gasterosteus aculeatus (Pisces: Gasterosteidae)

Heather A. Jamniczky, Emily E. Harper, Rebecca Garner, William A. Cresko, Peter C. Wainwright, Benedikt Hallgrimsson & Charles B. Kimmel
Phenotypes may evolve to become integrated in response to functional demands. Once evolved, integrated phenotypes, often modular, can also influence the trajectory of subsequent responses to selection. Clearly, connecting modularity and functionally adaptive evolution has been challenging. The teleost skull and jaw structures are useful for understanding this connection because of the key roles that these structures play in feeding in novel environments with different prey resources. In the present study, we examined such a...

Methods and data appendices for socioeconomic monitoring of nonmetropolitan communities following 25 years of the Northwest Forest Plan (1994–2018).

Michael R. Coughlan, Amelia Rhodeland & Heidi Huber-Stearns

Exposure to light changes soil chemical properties

Timothy Doane, Lucas Silva & William Horwath
Assessment of the effect of UV and visible light on the chemical properties of soils. Raw data of chemical properties measured in a laboratory study of a soils exposed to light.

Popocatepetl ash charge as function of humidity and temperature

Joshua Méndez Harper
Here, we provide the absolute charge collected by volcanic ash (Popocatepetl) in the range of 250-500 microns through frictional interactions as a function of relative humidity (RH) and temperature. The range of RH is 0-50% (at 25 C) and the range of temperature is -20-40 C (at 30 % RH). Particles were charged triboelectrically and the charge was measuirend on individual particles using a miniature Farday cup. All values are reported in pico-Coulombs.

Data from: Local adaptation to herbivory within tropical tree species along a rainfall gradient

Andrew Muehleisen, Bettina Engelbrecht, F. Andrew Jones, Eric Manzané-Pinzón & Liza Comita
In tropical forests, insect herbivores exert significant pressure on plant populations. Adaptation to such pressure is hypothesized to be a driver of high tropical diversity, but direct evidence for local adaptation to herbivory in tropical forests is sparse. At the same time, herbivore pressure has been hypothesized to increase with rainfall in the tropics, which could lead to differences among sites in the degree of local adaptation. To assess the presence of local adaptation and...

Data from: A phylum-wide survey reveals multiple independent gains of head regeneration in Nemertea

Eduardo Zattara, Fernando Fernández-Álvarez, Terra Hiebert, Alexa Bely & Jon Norenburg
Animals vary widely in their ability to regenerate, suggesting that regenerative ability has a rich evolutionary history. However, our understanding of this history remains limited because regenerative ability has only been evaluated in a tiny fraction of species. Available comparative regeneration studies have identified losses of regenerative ability, yet clear documentation of gains is lacking. We assessed ability to regenerate heads and tails either through our own experiments or from literature reports for 35 species...

Data from: Coevolutionary interactions with parasites constrain the spread of self-fertilization into outcrossing host populations

Samuel Preston Slowinski, Levi T. Morran, , Eric R. Cui, Amrita Bhattacharya, Curtis M. Lively, Patrick C. Phillips & Raymond C. Parrish
Given the cost of sex, outcrossing populations should be susceptible to invasion and replacement by self-fertilization or parthenogenesis. However, biparental sex is common in nature, suggesting that cross-fertilization has substantial short-term benefits. The Red Queen hypothesis (RQH) suggests that coevolution with parasites can generate persistent selection favoring both recombination and outcrossing in host populations. We tested the prediction that coevolving parasites can constrain the spread of self-fertilization relative to outcrossing. We introduced wild-type Caenorhabditis elegans...

Data from: Y-box protein 1 is required to sort microRNAs into exosomes in cells and in a cell-free reaction

Matthew J. Shurtleff, Morayma M. Temoche-Diaz, Kate V. Karfilis, Sayaka Ri & Randy Schekman
Exosomes are small vesicles that are secreted from metazoan cells and may convey selected membrane proteins and small RNAs to target cells for the control of cell migration, development and metastasis. To study the mechanisms of RNA packaging into exosomes, we devised a purification scheme based on the membrane marker CD63 to isolate a single exosome species secreted from HEK293T cells. Using immunoisolated CD63-containing exosomes we identified a set of miRNAs that are highly enriched...

Data from: Cryptic patterns of speciation in cryptic primates: microendemic mouse lemurs and the multispecies coalescent

Jelmer Poelstra, Jordi Salmona, George Tiley, Dominik Schüßler, Marina Blanco, Jean Andriambeloson, Olivier Bouchez, C. Ryan Campbell, Paul Etter, Amaia Iribar-Pelozuelo, Paul Hohenlohe, Kelsie Hunnicutt, Eric Johnson, Peter Kappeler, Peter Larsen, Sophie Manzi, Jose Ralison, Blanchard Randrianambinina, Rodin Rasoloarison, David Rasolofoson, Amanda Stahlke, David Weisrock, Rachel Williams, Lounes Chikhi, Ed Louis … & Anne Yoder
Species delimitation is ever more critical for assessing biodiversity in threatened regions of the world, especially when undescribed lineages may be at risk from habitat loss. Mouse lemurs (Microcebus) are an example of a rapid radiation of morphologically cryptic species that are distributed throughout Madagascar in its rapidly vanishing forested habitats. Here, we focus on two pairs of sister lineages that occur in a region in northeastern Madagascar that shows high levels of microendemism. We...

Data from: Inferring continuous and discrete population genetic structure across space

Gideon S. Bradburd, Graham M. Coop & Peter L. Ralph
A classic problem in population genetics is the characterization of discrete population structure in the presence of continuous patterns of genetic differentiation. Especially when sampling is discontinuous, the use of clustering or assignment methods may incorrectly ascribe differentiation due to continuous processes (e.g., geographic isolation by distance) to discrete processes, such as geographic, ecological, or reproductive barriers between populations. This reflects a shortcoming of current methods for inferring and visualizing population structure when applied to...

Data from: Intrinsic differences between males and females determine sex-specific consequences of inbreeding

Emily R. Ebel & Patrick C. Phillips
Background Inbreeding increases homozygosity and exposes deleterious recessive alleles, generally decreasing the fitness of inbred individuals. Interestingly, males and females are usually affected differently by inbreeding, though the more vulnerable sex depends on the species and trait measured. Results We used the soil-dwelling nematode Caenorhabditis remanei to examine sex-specific inbreeding depression across nine lineages, five levels of inbreeding, and hundreds of thousands of progeny. Female nematodes consistently suffered greater fitness losses than their male counterparts,...

Data from: Experimental evolution with Caenorhabditis nematodes

Henrique Teotónio, Suzanne Estes, Patrick C. Phillips & Charles F. Baer
The hermaphroditic nematode Caenorhabditis elegans has been one of the primary model systems in biology since the 1970s, but only within the last two decades has this nematode also become a useful model for experimental evolution. Here, we outline the goals and major foci of experimental evolution with C. elegans and related species, such as C. briggsae and C. remanei, by discussing the principles of experimental design, and highlighting the strengths and limitations of Caenorhabditis...

The Impact of COVID-19 on Journalism in Emerging Economies and the Global South

Damian Radcliffe

Data from: \"Identification of SNP markers for the endangered Ugandan red colobus (Procolobus rufomitratus tephrosceles) using RAD sequencing\" in Genomic Resources Notes accepted 1 December 2014 to 31 January 2015

Maria Jose Ruiz Lopez, Tony L. Goldberg, Colin A. Chapman, Patrick A. Omeja, James H. Jones, William M. Switzer, Paul D. Etter, Eric A. Johnson & Nelson Ting
Despite dramatic growth in the field of primate genomics over the past decade, studies of primate population and conservation genomics in the wild have been hampered due to the difficulties inherent in studying non-model organisms and endangered species, such as lack of a reference genome and current challenges in de novo primate genome assembly. Here, we used Restriction-site Associated DNA (RAD) sequencing to develop a population-based SNP panel for the Ugandan red colobus (P. rufomitratus...

Data from: Strong premating reproductive isolation drives incipient speciation in Mimulus aurantiacus

James M. Sobel & Matthew A. Streisfeld
Determining which forms of reproductive isolation have the biggest impact on the process of divergence is a major goal of speciation research. These barriers are often divided into those that affect the potential for hybridization (premating isolation), and those that occur after mating (postmating isolation), and much debate has surrounded the relative importance of these categories. Within the species Mimulus aurantiacus, red- and yellow-flowered ecotypes occur in the southwest corner of California, and a hybrid...

Data from: Linked morphological changes during palate evolution in early tetrapods

Charles B. Kimmel, Brian Sidlauskas & Jennifer A. Clack
We examined the shapes and sizes of dermal bones of the palate of selected Palaeozoic tetrapods in order to identify the ancestral states of palatal bone morphologies in the earliest tetrapods, to learn how the composition of the palate varies within and among early tetrapod radiations, and recognize evolutionary correlations among the size and shapes of skeletal elements in this important group of animals. We find that whereas the palatal bones themselves and their arrangements...

Data from: The Teleost Anatomy Ontology: anatomical representation for the genomics age

Wasila M. Dahdul, John G. Lundberg, Peter E. Midford, James P. Balhoff, Hilmar Lapp, Todd J. Vision, Melissa A. Haendel, Monte Westerfield & Paula M. Mabee
The rich knowledge of morphological variation among organisms reported in the systematic literature has remained in free-text format, impractical for use in large-scale synthetic phylogenetic work. This noncomputable format has also precluded linkage to the large knowledgebase of genomic, genetic, developmental, and phenotype data in model organism databases. We have undertaken an effort to prototype a curated, ontology-based evolutionary morphology database that maps to these genetic databases (http://kb.phenoscape.org) to facilitate investigation into the mechanistic basis...

Data from: A unified anatomy ontology of the vertebrate skeletal system

Wasila M. Dahdul, James P. Balhoff, David C. Blackburn, Alexander D. Diehl, Melissa A. Haendel, Brian K. Hall, Hilmar Lapp, John G. Lundberg, Christopher J. Mungall, Martin Ringwald, Erik Segerdell, Ceri E. Van Slyke, Matthew K. Vickaryous, Monte Westerfield & Paula M. Mabee
The skeleton is of fundamental importance in research in comparative vertebrate morphology, paleontology, biomechanics, developmental biology, and systematics. Motivated by research questions that require computational access to and comparative reasoning across the diverse skeletal phenotypes of vertebrates, we developed a module of anatomical concepts for the skeletal system, the Vertebrate Skeletal Anatomy Ontology (VSAO), to accommodate and unify the existing skeletal terminologies for the species-specific (mouse, the frog Xenopus, zebrafish) and multispecies (teleost, amphibian) vertebrate...

Data from: Links between plant and fungal diversity in habitat fragments of coastal shrubland

Mia R. Maltz, Kathleen K. Treseder & Krista L. McGuire
Habitat fragmentation is widespread across ecosystems, detrimentally affecting biodiversity. Although most habitat fragmentation studies have been conducted on macroscopic organisms, microbial communities and fungal processes may also be threatened by fragmentation. This study investigated whether fragmentation, and the effects of fragmentation on plants, altered fungal diversity and function within a fragmented shrubland in southern California. Using fluorimetric techniques, we assayed enzymes from plant litter collected from fragments of varying sizes to investigate enzymatic responses to...

Social Media in the Middle East: The Story of 2016: Top trends and data from the past 12 months

Damian Radcliffe

A new hypothesis for the origin of Amazonian Dark Earths [Data Set]

Lucas C. R. Silva

The Publisher’s Guide to Navigating COVID-19

Damian Radcliffe

Data from: Genetic correlations and the evolution of photoperiodic time measurement within a local population of the pitcher-plant mosquito, Wyeomyia smithii

William E. Bradshaw, Kevin J. Emerson & Christina M. Holzapfel
The genetic relationship between the daily circadian clock and the seasonal photoperiodic timer remains a subject of intense controversy. In Wyeomyia smithii, the critical photoperiod (an overt expression of the photoperiodic timer) evolves independently of the rhythmic response to the Nanda-Hamner protocol (an overt expression of the daily circadian clock) over a wide geographic range in North America. Herein, we focus on these two processes within a single local population in which there is a...

Data from: Thermal adaptation and acclimation of ectotherms from differing aquatic climates

Shawn R. Narum, Nathan R. Campbell, Kevin A. Meyer, Michael R. Miller & Ronald W. Hardy
To elucidate the mechanisms of thermal adaptation and acclimation in ectothermic aquatic organisms from differing climates, we used a common-garden experiment for thermal stress to investigate the heat shock response of redband trout (Oncorhynchus mykiss gairdneri) from desert and montane populations. Evidence for adaptation was observed as expression of heat shock genes in fish from the desert population was more similar to control (unstressed) fish and significantly different (P ≤ 0.05) from those from the...

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