454 Works

Musical Passage: A Voyage to 1688 Jamaica

Laurent Dubois, Garner David & Mary Caton Lingold

Cheilanthes ecuadorensis: A new species of Cheilanthes s.s. (Pteridaceae) from northern South America

Karla Sosa
Ongoing research on the taxonomically complex genus Cheilanthes (Pteridaceae; Cheilanthoideae) has resulted in the identification of a new species from Loja Province in Ecuador—Cheilanthes ecuadorensis, described and illustrated herein. Originally collected in 1988 and identified as C. cf. rufopunctata, C. ecuadorensis is clearly distinct from that species in having pubescent adaxial blade surfaces and narrow, poorly-differentiated false indusia. Among the South American species currently included in Cheilanthes, C. ecuadorensis is superficially most similar to C....

Efficient parallelization of tensor network contractions for simulating quantum computation

Cupjin Huang, Fang Zhang, Michael Newman, Xiaotong Ni, Dawei Ding, Junjie Cai, Xun Gao, Tenghui Wang, Feng Wu, Gengyan Zhang, Hsiang-Sheng Ku, Zhengxiong Tian, Junyin Wu, Haihong Xu, Huanjun Yu, Bo Yuan, Mario Szegedy, Yaoyun Shi, Hui-Hai Zhao, Chunqing Deng & Jianxin Chen
In this paper, we demonstrate a classical simulation framework for quantum computation by contracting tensor networks of sizes previously deemed out of reach. The main contribution of this work is a parallelization scheme called index slicing that breaks down an infeasibly large tensor network contraction task into smaller subtasks that can be executed fully in parallel, without interdependencies or intermediate communications. As a benchmarking example, we show that our algorithm can reduce the simulation of...

Feel-Sad TV

Blake K. Beaver
This article develops a theory of sadness pornographies in contemporary feel-sad television. Under the sad porn category, the essay explores a key sub-genre in contemporary serial dramas: trauma porn. The article is anchored in an affective analysis of two contemporary serials: Amazon's Transparent and NBC's This Is Us, both of which center multigenerational, familial trauma. Through a combined Berlantian and Spinozist optic, the essay attends to various episodes from the two serials to illuminate the...

Data from: Using the Phenoscape Knowledgebase to relate genetic perturbations to phenotypic evolution

Prashanti Manda, James P. Balhoff, Hilmar Lapp, Paula Mabee & Todd J. Vision
The abundance of phenotypic diversity among species can enrich our knowledge of development and genetics beyond the limits of variation that can be observed in model organisms. The Phenoscape Knowledgebase (KB) is designed to enable exploration and discovery of phenotypic variation among species. Because phenotypes in the KB are annotated using standard ontologies, evolutionary phenotypes can be compared with phenotypes from genetic perturbations in model organisms. To illustrate the power of this approach, we review...

Data from: Genetics of hybrid male sterility among strains and species in the Drosophila pseudoobscura species group

Shannon R. McDermott & Mohamed A. F. Noor
Taxa in the early stages of speciation may bear intraspecific allelic variation at loci conferring barrier traits in hybrids such as hybrid sterility. Additionally, hybridization may spread alleles that confer barrier traits to other taxa. Historically, few studies examine within- and between-species variation at loci conferring reproductive isolation. Here, we test for allelic variation within Drosophila persimilis and within the Bogota subspecies of D. pseudoobscura at regions previously shown to contribute to hybrid male sterility....

Data from: Chimpanzee fathers bias their behaviour towards their offspring

Carson M. Murray, Margaret A. Stanton, Elizabeth V. Lonsdorf, Emily E. Wroblewski & Anne E. Pusey
Promiscuous mating was traditionally thought to curtail paternal investment owing to the potential costs of providing care to unrelated infants. However, mounting evidence suggests that males in some promiscuous species can recognize offspring. In primates, evidence for paternal care exists in promiscuous Cercopithecines, but less is known about these patterns in other taxa. Here, we examine two hypotheses for paternal associations with lactating mothers in eastern chimpanzees (Pan troglodytes schweinfurthii): paternal effort, whereby males associate...

Data from: Song learning and cognitive ability are not consistently related in a songbird

Rindy C. Anderson, William A. Searcy, Susan Peters, Melissa Hughes, Adrienne L. DuBois & Stephen Nowicki
Learned aspects of song have been hypothesized to signal cognitive ability in songbirds. We tested this hypothesis in hand-reared song sparrows (Melospiza melodia) that were tutored with playback of adult songs during the critical period for song learning. The songs developed by the 19 male subjects were compared to the model songs to produce two measures of song learning: the proportion of notes copied from models and the average spectrogram cross-correlation between copied notes and...

Data from: Relative importance of abiotic, biotic, and disturbance drivers of plant community structure in the sagebrush steppe

Rachel M. Mitchell, Jonathan D. Bakker, John B. Vincent & G. Matt Davies
Abiotic conditions, biotic factors, and disturbances can act as filters that control community structure and composition. Understanding the relative importance of these drivers would allow us to understand and predict the causes and consequences of changes in community structure. We used long-term data (1989-2002) from the sagebrush steppe in Washington state, USA, to ask three questions: 1) What are the key drivers of community-level metrics of community structure? 2) Do community-level metrics and functional groups...

Data from: Divergent evolution and niche differentiation within the common peatmoss Sphagnum magellanicum

Narjes Yousefi, Kristian Hassel, Kjell Ivar Flatberg, Petri Kemppainen, Emiliano Trucchi, Arthur Jonathan Shaw, Magni Olsen Kyrkjeeide, Péter Szövényi & Hans Kristen Stenøien
PREMISE OF THE STUDY: Populations with phenotypic polymorphism in discrete characters may be good models for investigating genome evolution and speciation. Sphagnum magellanicum Brid. is found throughout the northern hemisphere, and despite considerable variation in morphological characters, it is considered one of the least taxonomically controversial peatmoss species. We have observed two main morphs of the species associated with different microhabitats. Here we investigated the genomic and environmental basis of this intraspecific morphological variation. METHODS:...

Data from: A genetic legacy of introgression confounds phylogeny and biogeography in oaks

John D. McVay, Andrew L. Hipp & Paul S. Manos
Oaks (Quercus L.) have long been suspected to hybridize in nature, and widespread genetic exchange between morphologically defined species is well documented in two- to six-species systems, but the phylogenetic consequences of hybridization in oaks have never been demonstrated in a phylogenetically diverse sample. Here, we present phylogenomic analyses of a ca 30 Myr clade that strongly support morphologically defined species and the resolution of novel clades of white oaks; however, historical hybridization across clade...

Data from: Gene signature of the human pancreatic ε-cell

Giselle Dominguez Gutierrez, Jinrang Kim, Ann-Hwee Lee, Jenny Tong, JingJing Niu, Sarah Gray, Yi Wei, Yueming Ding, Min Ni, Christina Adler, Andrew J. Murphy, Jesper Gromada, Yurong Xin & Sarah M Gray
The ghrelin producing ε-cell represents the fifth endocrine cell type in human pancreatic islets. The abundance of ε-cells in adult pancreas is extremely low, which has hampered the investigation on the molecular pathways regulating the development and the function of this cell type. In this study, we explored the molecular features defining the function of pancreatic ε-cells isolated from adult non-diabetic donors using single-cell RNA sequencing technology. We focus on transcription factors, cell surface receptors...

Data from: Dissecting the role of a large chromosomal inversion in life history divergence throughout the Mimulus guttatus species complex

Jennifer M. Coughlan & John H. Willis
Chromosomal inversions can play an important role in adaptation, but the mechanism of their action in many natural populations remains unclear. An inversion could suppress recombination between locally beneficial alleles, thereby preventing maladaptive reshuffling with less-fit, migrant alleles. The recombination suppression hypothesis has gained much theoretical support but empirical tests are lacking. Here, we evaluated the evolutionary history and phenotypic effects of a chromosomal inversion which differentiates annual and perennial forms of Mimulus guttatus. We...

Data from: Genetic architecture of quantitative flower and leaf traits in a pair of sympatric sister species of Primulina

Chen Feng, Chao Feng, Lihua Yang, Ming Kang & Mark D. Rausher
Flowers and leaves each represent suites of functionally interrelated traits that are often involved in species divergence and local adaptation. However, a major unresolved issue is how the individual component traits that make up a complex trait such as a flower evolve in a coordinated fashion to retain a high degree of functionality. We use a quantitative trait loci (QTL) approach to elucidate the genetic architecture of divergence in flower and leaf traits between sister...

Data from: Extremely long-distance seed dispersal by an overfished Amazonian frugivore

Jill T. Anderson, Tim Nuttle, Joe S. Saldaña Rojas, Thomas H. Pendergast & Alexander S. Flecker
Throughout Amazonia, overfishing has decimated populations of fruit-eating fishes, especially the largebodied characid, Colossoma macropomum. During lengthy annual floods, frugivorous fishes enter vast Amazonian floodplains, consume massive quantities of fallen fruits and egest viable seeds. Many tree and liana species are clearly specialized for icthyochory, and seed dispersal by fish may be crucial for the maintenance of Amazonian wetland forests. Unlike frugivorous mammals and birds, little is known about seed dispersal effectiveness of fishes. Extensive...

Data from: Genetic and evolutionary correlates of fine-scale recombination rate variation in Drosophila persimilis

Laurie S. Stevison & Mohamed A. F. Noor
Recombination is fundamental to meiosis in many species and generates variation on which natural selection can act, yet fine-scale linkage maps are cumbersome to construct. We generated a fine-scale map of recombination rates across two major chromosomes in Drosophila persimilis using 181 SNP markers spanning two of five major chromosome arms. Using this map, we report significant fine-scale heterogeneity of local recombination rates. However, we also observed “recombinational neighborhoods,” where adjacent intervals had similar recombination...

Data from: The genetic architecture of biofilm formation in a clinical isolate of Saccharomyces cerevisiae

Joshua A. Granek, Debra Murray, Ömür Kayıkçı & Paul M. Magwene
Biofilms are microbial communities that form on surfaces. They are the primary form of microbial growth in nature and can have detrimental impacts on human health. Some strains of the budding yeast Saccharomyces cerevisiae form colony biofilms, and there is substantial variation in colony architecture between biofilm-forming strains. To identify the genetic basis of biofilm variation, we developed a novel version of quantitative trait locus mapping, which leverages cryptic variation in a clinical isolate of...

Data from: Data reuse and the open data citation advantage

Heather A. Piwowar & Todd J. Vision
Background: Attribution to the original contributor upon reuse of published data is important both as a reward for data creators and to document the provenance of research findings. Previous studies have found that papers with publicly available datasets receive a higher number of citations than similar studies without available data. However, few previous analyses have had the statistical power to control for the many variables known to predict citation rate, which has led to uncertain...

Data from: Postcranial morphology and the locomotor habits of living and extinct carnivorans

Joshua X. Samuels, Julie A. Meachen & Stacey A. Sakai
Members of the order Carnivora display a broad range of locomotor habits, including cursorial, scansorial, arboreal, semiaquatic, aquatic, and semifossorial species from multiple families. Ecomorphological analyses from osteological measurements have been used successfully in prior studies of carnivorans and rodents to accurately infer the locomotor habits of extinct species. This study uses 20 postcranial measurements that have been shown to be effective indicators of locomotor habits in rodents and incorporates an extensive sample of over...

Data from: Global biogeography of scaly tree ferns (Cyatheaceae): evidence for Gondwanan vicariance and limited transoceanic dispersal

Petra Korall & Kathleen M. Pryer
Aim: Scaly tree ferns, Cyatheaceae, are a well-supported group of mostly tree-forming ferns found throughout the tropics, the subtropics and the south-temperate zone. Fossil evidence shows that the lineage originated in the Late Jurassic period. We reconstructed large-scale historical biogeographical patterns of Cyatheaceae and tested the hypothesis that some of the observed distribution patterns are in fact compatible, in time and space, with a vicariance scenario related to the break-up of Gondwana. Location: Tropics, subtropics...

Data from: How hot are Drosophila hotspots? Examining recombination rate variation and associations with nucleotide diversity, divergence, and maternal age in Drosophila pseudoobscura

Brenda Manzano-Winkler, Suzanne E. McGaugh & Mohamed A. F. Noor
Fine scale meiotic recombination maps have uncovered a large amount of variation in crossover rate across the genomes of many species, and such variation in mammalian and yeast genomes is concentrated to <5 kb regions of highly elevated recombination rates (10–100x the background rate) called “hotspots.” Drosophila exhibit substantial recombination rate heterogeneity across their genome, but evidence for these highly-localized hotspots is lacking. We assayed recombination across a 40 Kb region of Drosophila pseudoobscura chromosome...

Data from: Stasis and convergence characterize morphological evolution in eupolypod II ferns

Michael A. Sundue & Carl J. Rothfels
Background and Aims: Patterns of morphological evolution at levels above family rank remain underexplored in the ferns. The present study seeks to address this gap through analysis of 79 morphological characters for 81 taxa, including representatives of all ten families of eupolypod II ferns. Recent molecular phylogenetic studies demonstrate that the evolution of the large eupolypod II clade (which includes nearly one-third of extant fern species) features unexpected patterns. The traditional ‘athyrioid’ ferns are scattered...

Data from: Integrative taxonomy resolves the cryptic and pseudo-cryptic Radula buccinifera complex (Porellales: Jungermanniopsida), including two reinstated and five new species

Matt A. M. Renner, Nicolas Devos, Jairo Patiño, Elizabeth A. Brown, Andrew Orme, Michael Elgy, Trevor Wilson, Lindsey J. Gray, Matt J. Von Konrat, Lindsey Gray, Matt Renner, Elizabeth Brown & Matt Von Konrat
Molecular data from three chloroplast markers resolve individuals attributable to Radula buccinifera in six lineages belonging to two subgenera, indicating the species is polyphyletic as currently circumscribed. All lineages are morphologically diagnosable, but one pair exhibits such morphological overlap that they can be considered cryptic. Molecular and morphological data justify the re-instatement of a broadly circumscribed ecologically variable R. strangulata, of R. mittenii, and the description of five new species. Two species Radula mittenii Steph....

Data from: Strong selection genome-wide enhances fitness trade-offs across environments and episodes of selection

Jill Theresa Anderson, Cheng-Ruei Lee & Thomas Mitchell-Olds
Fitness trade-offs across episodes of selection and environments influence life-history evolution and adaptive population divergence. Documenting these trade-offs remains challenging as selection can vary in magnitude and direction through time and space. Here, we evaluate fitness trade-offs at the levels of the whole organism and the quantitative trait locus (QTL) in a multiyear field study of Boechera stricta (Brassicaceae), a genetically tractable mustard native to the Rocky Mountains. Reciprocal local adaptation was pronounced for viability,...

Data from: Defining spatial and temporal patterns of phylogeographic structure in Madagascar's iguanid lizards (Genus Oplurus)

Lauren M. Chan, Dean Choi, Achille P. Raselimanana, Hery A. Rakotondravony & Anne D. Yoder
Understanding the remarkably high species diversity and levels of endemism found among Madagascar’s flora and fauna has been the focus of many studies. One hypothesis that has received much attention proposes that Pleistocene climate fluctuations spurred diversification. However, while spatial patterns of distribution and phylogenetic relationships can provide support for biogeographic predictions, temporal estimates of divergence are required to determine the fit of these geospatial patterns to climatic or biogeographic mechanisms. We use multilocus DNA...

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