20 Works

Data from: Single nucleotide polymorphism discovery via genotyping by sequencing to assess population genetic structure and recurrent polyploidization in Andropogon gerardii

Christine McAllister, Allison J. Miller & Christine A. McAllister
Premise of the study. Autopolyploidy, genome duplication within a single lineage, can result in multiple cytotypes within a species. Geographic distributions of cytotypes may reflect the evolutionary history of autopolyploid formation and subsequent population dynamics including stochastic (drift) and deterministic (differential selection among cytotypes) processes. Here, we used a population genomic approach to investigate whether autopolyploidy occurred once or multiple times in Andropogon gerardii, a widespread, North American grass with two predominant cytotypes. Methods. Genotyping-by-sequencing...

Patterns of thermal sensitivity and sex-specificity of courtship behavior differs between two sympatric species of Enchenopa treehopper

Anthony Macchiano, Daniel A. Sasson, Noah T. Leith & Kasey D. Fowler-Finn
Predicting how insects will react to future thermal conditions requires understanding how temperature currently affects insect behavior, from performance traits to those involved in mating and reproduction. Many reproductive behaviors are thermally-sensitive, but little is known how temperature affects the behaviors used to find mates and coordinate mating. Here, we investigate how temperature influences courtship activity in two sympatric species of Enchenopa treehoppers (Hemiptera: Membracidae). Enchenopa use substrate-borne vibrational signals exchanged in male-female duets to...

Data from: DNA barcodes of the native ray-finned fishes in Taiwan

Chia-Hao Chang, Kwang-Tsao Shao, Han-Yang Lin, Yung-Chieh Chui, Mao-Ying Lee, Shih-Hui Liu, Pai-Lei Lin & Yung-Chieh Chiu
Species identification based on the DNA sequence of a fragment of the cytochrome c oxidase subunit I (COI) gene in the mitochondrial genome, DNA barcoding, is widely applied to assist in sustainable exploitation of fish resources and the protection of fish biodiversity. The aim of this study was to establish a reliable barcoding reference database of the native ray-finned fishes in Taiwan. A total of 2,993 individuals, belonging to 1,245 species within 637 genera, 184...

Data from: Niche opportunities and invasion dynamics in a desert annual community

Ginger R. H. Allington, Thomas J. Valone, David N. Koons, S. K. Morgan Ernest & Michele R. Schutzenhofer
Although many factors influence the ability of exotics to invade successfully, most studies focus on only a few variables to explain invasion; attempts at theoretical synthesis are largely untested. The niche opportunities framework proposes that the demographic success of an invader is largely affected by the availability of resources and the abundance of its enemies. Here, we use a 31-year study from a desert ecosystem to examine the niche opportunities framework via the invasion of...

Data from: Population genomics of wild and laboratory zebrafish (Danio rerio)

Andrew R Whiteley, Anuradha Bhat, Emilia P Martins, Richard L Mayden, M Arunachalam, Silva Uusi-Heikkilä, A.T.A. Ahmed, Jiwan Shrestha, Matthew Clark, Derek Stemple & Louis Bernatchez
Understanding a wider range of genotype-phenotype associations can be achieved through ecological and evolutionary studies of traditional laboratory models. Here, we conducted the first large-scale geographic analysis of genetic variation within and among wild zebrafish (Danio rerio) populations occurring in Nepal, India, and Bangladesh and we genetically compared wild populations to several commonly used lab strains. We examined genetic variation at 1,832 polymorphic EST-based SNPs and the cytb mitochondrial gene in 13 wild populations and...

Data from: Health insurance coverage with or without a nurse-led task shifting strategy for hypertension control: a pragmatic cluster randomized trial in Ghana

Gbenga Ogedegbe, Jacob Plange-Rhule, Joyce Gyamfi, William Chaplin, Michael Ntim, Kingsley Apusiga, Juliet Iwelunmor, Kwasi Yeboah Awudzi, Kofi Nana Quakyi, Jazmin N. Mogavero, Kiran Khurshid, Bamidele Tayo & Richard Cooper
Rationale: Poor access to care and physician shortage are major barriers to hypertension control in sub-Saharan Africa. Implementation of evidence-based systems-level strategies targeted at these barriers are lacking. Objective: To evaluate the comparative effectiveness of provision of health insurance coverage (HIC) alone versus a nurse-led task-shifting strategy for hypertension control (TASSH) plus HIC on systolic BP reduction among patients with uncontrolled hypertension in Ghana. Methods and Findings: Using a pragmatic cluster-randomized trial, 32 community health...

Data from: Climate and local abundance in freshwater fishes

Jason H. Knouft & Melissa M. Anthony
Identifying factors regulating variation in numbers of individuals among populations across a species' distribution is a fundamental goal in ecology. A common prediction, often referred to as the abundant-centre hypothesis, suggests that abundance is highest near the centre of a species' range. However, because of the primary focus on the geographical position of a population, this framework provides little insight into the environmental factors regulating local abundance. While range-wide variation in population abundance associated with...

Data from: Molecular phylogeny of the cyprinid tribe Labeonini (Teleostei: Cypriniformes)

Lei Yang, M. Arunachalam, Tetsuya Sado, Boris A. Levin, Alexander S. Golubtsov, Jörg Freyhof, John P. Friel, Wei-Jen Chen, M. Vincent Hirt, Raja Manickam, Mary K. Agnew, Andrew M. Simons, Kenji Saitoh, Masaki Miya, Richard L. Mayden & Shunping He
The cyprinid tribe Labeonini (sensu Rainboth, 1991) is a large group of freshwater fishes containing around 40 genera and 400 species. They are characterized by an amazing diversity of modifications to their lips and associated structures. In this study, a total of 34 genera and 142 species of putative members of this tribe, which represent most of the generic diversity and more than one third of the species diversity of the group, were sampled and...

Data from: Evolutionary origin and early biogeography of otophysan fishes (Ostariophysi: Teleostei)

Wei-Jen Chen, Sébastien Lavoué & Richard L. Mayden
Biogeography of the mega-diverse, freshwater and globally-distributed Otophysi has received considerable attention. The attraction largely stems from assumptions as its ancient origin, and by being almost exclusively freshwater, their suitability as to explanations of trans-oceanic distributions. Despite multiple hypotheses explaining present-day distributions, problems remain, precluding more parsimonious explanations. Underlying previous hypotheses involve alternative phylogenies for Otophysi, uncertainties as to temporal diversification and assumptions integral to various explanations. We reexamine the origin and early diversification of...

Data From: TERRA-REF, An open reference data set from high resolution genomics, phenomics, and imaging sensors

David LeBauer, Burnette Maxwell, Jeffrey Demieville, Noah Fahlgren, Andrew French, Roman Garnett, Zhenbin Hu, Kimberly Huynh, Rob Kooper, Zongyang Li, Maitiniyazi Maimaitijiang, Jerome Mao, Todd Mockler, Geoffrey Morris, Maria Newcomb, Michael Ottman, Philip Ozersky, Sidike Paheding, Duke Pauli, Robert Pless, Wei Qin, Kristina Riemer, Gareth Rohde, William Rooney, Vasit Sagan … & Charles Zender
The ARPA-E funded TERRA-REF project is generating open-access reference datasets for the study of plant sensing, genomics, and phenomics. Sensor data were generated by a field scanner sensing platform that captures color, thermal, hyperspectral, and active flourescence imagery as well as three dimensional structure and associated environmental measurements. This dataset is provided alongside data collected using traditional field methods in order to support calibration and validation of algorithms used to extract plot level phenotypes from...

Data from: Genetic structure of Pacific trout at the extreme southern end of their native range

Alicia Abadía-Cardoso, John Carlos Garza, Richard L. Mayden & Francisco Javier García De León
Salmonid fishes are cold water piscivores with a native distribution spanning nearly the entire temperate and subarctic northern hemisphere. Trout in the genus Oncorhynchus are the most widespread salmonid fishes and are among the most important fish species in the world, due to their extensive use in aquaculture and valuable fisheries. Trout that inhabit northwestern Mexico are the southernmost native salmonid populations in the world, and the least studied in North America. They are unfortunately...

Data from: Bee communities along a prairie restoration chronosequence: similar abundance and diversity, distinct composition

Rebecca K. Tonietto, John S. Ascher & Daniel J. Larkin
Recognition of the importance of bee conservation has grown in response to declines of managed honey bees and some wild bee species. Habitat loss has been implicated as a leading cause of declines, suggesting that ecological restoration is likely to play an increasing role in bee conservation efforts. In the Midwestern USA, restoration of tallgrass prairie has traditionally targeted plant community objectives without explicit consideration for bees. However, restoration of prairie vegetation is likely to...

Data from: Mechanical factors direct mouse aortic remodeling during early maturation

Victoria P. Le, Jeffrey K. Cheng, Jungsil Kim, Marius C. Staiculescu, Shawn W. Ficker, Saahil C. Sheth, Siddharth A. Bhayani, Robert P. Mecham, Hiromi Yanagisawa & Jessica E. Wagenseil
Numerous diseases have been linked to genetic mutations that lead to reduced amounts or disorganization of arterial elastic fibres. Previous work has shown that mice with reduced amounts of elastin (Eln+/−) are able to live a normal lifespan through cardiovascular adaptations, including changes in haemodynamic stresses, arterial geometry and arterial wall mechanics. It is not known if the timeline and presence of these adaptations are consistent in other mouse models of elastic fibre disease, such...

Data from: Vitis phylogenomics: hybridization intensities from a SNP array outperform genotype calls

Allison J. Miller, Naim Matasci, Heidi Schwaninger, Mallikarjuna K. Aradhya, Bernard Prins, Gan-Yuan Zhong, Charles Simon, Edward S. Buckler & Sean Myles
Understanding relationships among species is a fundamental goal of evolutionary biology. Single nucleotide polymorphisms (SNPs) identified through next generation sequencing and related technologies enable phylogeny reconstruction by providing unprecedented numbers of characters for analysis. One approach to SNP-based phylogeny reconstruction is to identify SNPs in a subset of individuals, and then to compile SNPs on an array that can be used to genotype additional samples at hundreds or thousands of sites simultaneously. Although powerful and...

Data from: Evolution of phenotype-environment associations by genetic responses to selection and phenotypic plasticity in a temporally autocorrelated environment

Matt J. Michel, Luis-Miguel Chevin & Jason H. Knouft
Covariation between population-mean phenotypes and environmental variables, sometimes termed a ‘phenotype-environment association’ (PEA), can result from phenotypic plasticity, genetic responses to natural selection, or both. PEAs can potentially provide information on the evolutionary dynamics of a particular set of populations, but this requires a full theoretical characterization of PEAs and their evolution. Here, we derive formulas for the expected PEA in a temporally fluctuating environment for a quantitative trait with a linear reaction norm. We...

Data from: Influence of introgression and geological processes on phylogenetic relationships of western North American mountain suckers (Pantosteus, Catostomidae)

Peter J. Unmack, Thomas E. Dowling, Nina J. Laitinen, Carol L. Secor, Richard L. Mayden, Dennis K. Shiozawa & Gerald R. Smith
Intense geological activity caused major topographic changes in Western North America over the past 15 million years. Major rivers here are composites of different ancient rivers, resulting in isolation and mixing episodes between river basins over time. This history influenced the diversification of most of the aquatic fauna. The genus Pantosteus is one of several clades centered in this tectonically active region. The eight recognized Pantosteus species are widespread and common across southwestern Canada, western...

Data from: Prior information and social experience influence male reproductive decisions

Jesse Balaban-Feld & Thomas J. Valone
Increasing attention has focused on understanding how past experiences can influence and explain variation in mating preferences among individuals. We examined how previous social experiences affected courtship preferences in Drosophila melanogaster by exposing individual males to different frequency distributions of high- and low-quality (HQ and LQ) females and by allowing them to copulate with either a HQ or LQ mate. For a male, a large female represents a high-quality mate while a small female is...

Data from: Local population density and group composition influence signal-preference relationships in Enchenopa treehoppers (Hemiptera: Membracidae)

Kasey D. Fowler-Finn, Daniel C. Cruz & Rafael L. Rodriguez
Many animals exhibit social plasticity—changes in phenotype or behavior in response to experience with conspecifics—that change how evolutionary processes like sexual selection play out. Here, we asked whether social plasticity arising from variation in local population density in male advertisement signals and female mate preferences influences the form of sexual selection. We manipulated local density and determined whether this changed how the distribution of male signals overlapped with female preferences—i.e., the signal-mate preference relationship. We...

Data from: Multispecies conservation of freshwater fish assemblages in response to climate change in the southeastern United States

Michelle VanCompernolle, Jason H. Knouft & Darren L. Ficklin
Aim: Streamflow and water temperature are primary variables influencing the distribution of freshwater taxa. Climate-induced changes in these variables are already causing shifts in species distributions, with continued changes projected in the coming decades. The Mobile River Basin (MRB), located in the southeastern United States, contains some of the highest levels of temperate freshwater biodiversity in North America. We integrated species distribution data with contemporary and future streamflow and water temperature data as well as...

RAD-seq reveals patterns of diversification, hybridization, and the accumulation of reproductive isolation in a clade of partially sympatric, tropical island trees

Alexander Linan, , Allison Miller, George Schatz, Jean Claude Sevathian & Christine Edwards
A common pattern observed in temperate tree clades is that species are often morphologically distinct and partially interfertile but maintain species cohesion despite ongoing hybridization where ranges overlap. Although closely related species commonly occur in sympatry in tropical ecosystems, little is known about patterns of hybridization within a clade over time, and the implications of this hybridization for the maintenance of species boundaries. In this study, we focused on a clade of sympatric trees in...

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