25 Works

Data from: Remarkably divergent regions punctuate the genome assembly of the Caenorhabditis elegans Hawaiian strain CB4856

Owen A. Thompson, L. Basten Snoek, Harm Nijveen, Mark G. Sterken, Rita J. M. Volkers, Rachel Brenchley, Arjen Van't Hof, Roel P. J. Bevers, Andrew R. Cossins, Itai Yanai, Alex Hajnal, Tobias Schmid, Jaryn D. Perkins, David Spencer, Leonid Kruglyak, Erik C. Andersen, Donald G. Moerman, LaDeana W. Hillier, Jan E. Kammenga & Robert H. Waterston
The Hawaiian strain (CB4856) of Caenorhabditis elegans is one of the most divergent from the canonical laboratory strain N2 and has been widely used in developmental, population and evolutionary studies. To enhance the utility of the strain, we have generated a draft sequence of the CB4856 genome, exploiting a variety of resources and strategies. The CB4856 genome when compared against the N2 reference has 327,050 single nucleotide variants (SNVs) and 79,529 insertion-deletion events (indels) that...

Data from: Temporal genetic analysis of the endangered tidewater goby: metapopulation dynamics or drift in isolation?

Andrew P. Kinziger, Michael Hellmair, William Tyler McCraney, David K. Jacobs & Greg Goldsmith
Extinction and colonization dynamics are critical to understanding the evolution and conservation of metapopulations. However, traditional field studies of extinction–colonization are potentially fraught with detection bias and have rarely been validated. Here, we provide a comparison of molecular and field-based approaches for assessment of the extinction–colonization dynamics of tidewater goby (Eucyclogobius newberryi) in northern California. Our analysis of temporal genetic variation across 14 northern California tidewater goby populations failed to recover genetic change expected with...

Data from: Olfaction contributes to pelagic navigation in a coastal shark

Andrew P. Nosal, Yi Chao, John D. Farrara, Fei Chai & Philip A. Hastings
How animals navigate the constantly moving and visually uniform pelagic realm, often along straight paths between distant sites, is an enduring mystery. The mechanisms enabling pelagic navigation in cartilaginous fishes are particularly understudied. We used shoreward navigation by leopard sharks (Triakis semifasciata) as a model system to test whether olfaction contributes to pelagic navigation. Leopard sharks were captured alongshore, transported 9 km offshore, released, and acoustically tracked for approximately 4 h each until the transmitter...

Data from: Developmental plasticity affects sexual size dimorphism in an anole lizard

Camille Bonneaud, Erin Marnocha, Anthony Herrel, Bieke Vanhooydonck, Duncan J. Irschick & Thomas B. Smith
While developmental plasticity has been shown to contribute to sexual size dimorphism (SSD) in laboratory studies, its role in shaping SSD variation in wild vertebrate populations is unclear. Here we use a field study and a laboratory experiment to show that resource availability influences the degree of SSD among insular populations of Anolis sagrei lizards in the Bahamas. Total amounts of food biomass explained variation in male, but not female, body size on six Bahamian...

Data from: Seasonal polyphenism in wing coloration affects species recognition in rubyspot damselflies (Hetaerina spp.)

Jonathan P. Drury, Christopher N. Anderson & Gregory F. Grether
Understanding how phenotypic plasticity evolves and in turn affects the course of evolution is a major challenge in modern biology. By definition, biological species are reproductively isolated, but many animals fail to distinguish between conspecifics and closely related heterospecifics. In some cases, phenotypic plasticity may interfere with species recognition. Here, we document a seasonal polyphenism in the degree of dark wing pigmentation in smoky rubyspot damselflies (Hetaerina titia) – a shift so pronounced that it...

Data from: The legacy effects of keystone individuals on collective behavior scale to how long they remain within a group

Jonathan N. Pruitt & Noa Pinter-Wollman
The collective behaviour of social groups is often strongly influenced by one or few individuals, termed here ‘keystone individuals’. We examined whether the influence of keystone individuals on collective behaviour lingers after their departure and whether these lingering effects scale with their tenure in the group. In the social spider, Stegodyphus dumicola, colonies' boldest individuals wield a disproportionately large influence over colony behaviour. We experimentally manipulated keystones' tenure in laboratory-housed colonies and tracked their legacy...

Data from: Nest shape explains variation in sexual dichromatism in New World blackbirds

Jonathan P. Drury & Nathan Burroughs
Following Charles Darwin, research on sexual dichromatism has long focused on sexual selection driving ornamentation in males. However, Alfred Russel Wallace proposed another explanation – that dichromatism evolves as a result of selection favoring crypsis in incubating females. Many recent studies suggest that evolutionary changes in sexual dichromatism often result from changes in female, in addition to male, plumage, yet the evolutionary mechanisms driving changes in female plumage remain largely unexplained. To test Wallace's hypothesis,...

Data from: Evolutionary patterns of adaptive acrobatics and physical performance predict expression profiles of androgen receptor – but not oestrogen receptor – in the forelimb musculature

Matthew J. Fuxjager, Joy Eaton, Willow R. Lindsay, Lucie H. Salwiczek, Michelle A. Rensel, Julia Barske, Laurie Sorenson, Lainy B. Day & Barney A. Schlinger
1. Superior physical competence is vital to the adaptive behavioural routines of many animals, particularly those that engage in elaborate sociosexual displays. How such traits evolve across species remains unclear. 2. Recent work suggests that activation of sex steroid receptors in neuromuscular systems is necessary for the fine motor skills needed to execute physically elaborate displays. Thus, using passerine birds as models, we test whether interspecific variation in display complexity predicts species differences in the...

Data from: The concerted impact of domestication and transposon insertions on methylation patterns between dogs and grey wolves

Ilana Janowitz Koch, Michelle M. Creek, Michael J. Thompson, Kerry A. Deere-Machemer, Jun Wang, Lionel Duarte, Gitanjali E. Gnanadesikan, Eskender L. McCoy, Liudmilla Rubbi, Daniel R. Stahler, Matteo Pellegrini, Elaine A. Ostrander, Robert K. Wayne, Janet S. Sinsheimer, Bridgett M. VonHoldt & Michelle M. Clark
The process of domestication can exert intense trait-targeted selection on genes and regulatory regions. Specifically, rapid shifts in the structure and sequence of genomic regulatory elements could provide an explanation for the extensive, and sometimes extreme, variation in phenotypic traits observed in domesticated species. Here, we explored methylation differences from >24 000 cytosines distributed across the genomes of the domesticated dog (Canis familiaris) and the grey wolf (Canis lupus). PCA and model-based cluster analyses identified...

Data from: The good, the bad and the Ulva: the density dependent role of macroalgal subsidies in influencing diversity and trophic structure of an estuarine community

Lauri R. Green & Peggy M. Fong
Worldwide, ecological subsidies enhance ecosystem productivity and therefore trophic support for greater biodiversity of taxa. While studies in terrestrial and aquatic ecosystems demonstrate that the magnitude of subsidies into ecosystems differs widely, the thresholds where subsidies may switch from exerting positive to negative effects are poorly understood. In estuaries, eutrophication promotes drift macroalgae that deposit on the benthos, cover intertidal flats for months and serve as pressed resource subsidies for benthic consumers. We hypothesized there...

Data from: Seascape drivers of Macrocystis pyrifera population genetic structure in the northeast Pacific

Mattias L. Johansson, Filipe Alberto, Daniel C. Reed, Peter T. Raimondi, Nelson C. Coelho, Mary A. Young, Patrick T. Drake, Christopher A. Edwards, Kyle Cavanaugh, Jorge Assis, Lydia B. Ladah, Tom W. Bell, James A. Coyer, David A. Siegel & Ester A. Serrão
At small spatial and temporal scales, genetic differentiation is largely controlled by constraints on gene flow, while genetic diversity across a species' distribution is shaped on longer temporal and spatial scales. We assess the hypothesis that oceanographic transport and other seascape features explain different scales of genetic structure of giant kelp, Macrocystis pyrifera. We followed a hierarchical approach to perform a microsatellite-based analysis of genetic differentiation in Macrocystis across its distribution in the northeast Pacific....

Data from: Global circulation patterns of seasonal influenza viruses vary with antigenic drift

Trevor Bedford, Steven Riley, Ian G. Barr, Shobha Broor, Mandeep Chadha, Nancy J. Cox, Rodney S. Daniels, C. Palani Gunasekaran, Aeron C. Hurt, Anne Kelso, Alexander Klimov, Nicola S. Lewis, Xiyan Li, John W. McCauley, Takato Odagiri, Varsha Potdar, Andrew Rambaut, Yuelong Shu, Eugene Skepner, Derek J. Smith, Marc A. Suchard, Masato Tashiro, Dayan Wang, Xiyan Xu, Philippe Lemey … & Colin A. Russell
Understanding the spatiotemporal patterns of emergence and circulation of new human seasonal influenza virus variants is a key scientific and public health challenge. The global circulation patterns of influenza A/H3N2 viruses are well characterized1, 2, 3, 4, 5, 6, 7, but the patterns of A/H1N1 and B viruses have remained largely unexplored. Here we show that the global circulation patterns of A/H1N1 (up to 2009), B/Victoria, and B/Yamagata viruses differ substantially from those of A/H3N2...

Data from: Targeted capture and resequencing of 1040 genes reveal environmentally driven functional variation in gray wolves

Rena M. Schweizer, Jacqueline Robinson, Ryan Harrigan, Pedro Silva, Marco Galaverni, Marco Musiani, Richard E. Green, John Novembre & Robert K. Wayne
In an era of ever-increasing amounts of whole genome sequence data for individuals and populations, the utility of traditional single nucleotide polymorphisms (SNPs) array-based genome scans is uncertain. We previously performed a SNP array-based genome scan to identify candidate genes under selection in six distinct gray wolf (Canis lupus) ecotypes. Using this information, we designed a targeted capture array for 1040 genes, including all exons and flanking regions, as well as 5000 1 kb non-genic...

Data from: Optical data compression in time stretch imaging

Claire Lifan Chen, Ata Mahjourbar, Bahram Jalali & Ata Mahjoubfar
Time stretch imaging offers real-time image acquisition at millions of frames per second and subnanosecond shutter speed, and has enabled detection of rare cancer cells in blood with record throughput and specificity. An unintended consequence of high throughput image acquisition is the massive amount of digital data generated by the instrument. Here we report the first experimental demonstration of real-time optical image compression applied to time stretch imaging. By exploiting the sparsity of the image,...

Data from: Genome-wide signature of local adaptation linked to variable CpG methylation in oak populations

Alexander Platt, Paul F. Gugger, Victoria L. Sork & Matteo Pellegrini
It has long been known that adaptive evolution can occur through genetic mutations in DNA sequence, but it is unclear whether adaptive evolution can occur through analogous epigenetic mechanisms, such as through DNA methylation. If epigenetic variation contributes directly to evolution, species under threat of disease, invasive competition, climate change or other stresses would have greater stores of variation from which to draw. We looked for evidence of natural selection acting on variably methylated DNA...

Data from: Detecting recent selective sweeps while controlling for mutation rate and background selection

Christian D. Huber, Michael DeGiorgio, Ines Hellmann & Rasmus Nielsen
A composite likelihood ratio test implemented in the program SweepFinder is a commonly used method for scanning a genome for recent selective sweeps. SweepFinder uses information on the spatial pattern (along the chromosome) of the site frequency spectrum (SFS) around the selected locus. To avoid confounding effects of background selection and variation in the mutation process along the genome, the method is typically applied only to sites that are variable within species. However, the power...

Data from: Crowdsourced geometric morphometrics enable rapid large-scale collection and analysis of phenotypic data

Jonathan Chang & Michael E. Alfaro
1. Advances in genomics and informatics have enabled the production of large phylogenetic trees. However, the ability to collect large phenotypic datasets has not kept pace. 2. Here, we present a method to quickly and accurately gather morphometric data using crowdsourced image-based landmarking. 3. We find that crowdsourced workers perform similarly to experienced morphologists on the same digitization tasks. We also demonstrate the speed and accuracy of our method on seven families of ray-finned fishes...

Data from: Reproductive interference explains persistence of aggression between species

Jonathan P. Drury, Kenichi W. Okamoto, Christopher N. Anderson & Gregory F. Grether
Interspecific territoriality occurs when individuals of different species fight over space, and may arise spontaneously when populations of closely related territorial species first come into contact. But defence of space is costly, and unless the benefits of excluding heterospecifics exceed the costs, natural selection should favour divergence in competitor recognition until the species no longer interact aggressively. Ordinarily males of different species do not compete for mates, but when males cannot distinguish females of sympatric...

Data from: Simulation as a new tool to establish benchmark outcome measures in obstetrics

Matt M. Kurrek, Pamela Morgan, Steven Howard, Peter Kranke, Aaron Calhoun, Joshua Hui & Alex Kiss
Background: There are not enough clinical data from rare critical events to calculate statistics to decide if the management of actual events might be below what could reasonably be expected (i.e. was an outlier). Objectives: In this project we used simulation to describe the distribution of management times as an approach to decide if the management of a simulated obstetrical crisis scenario could be considered an outlier. Design: Twelve obstetrical teams managed 4 scenarios that...

Data from: Genetic subdivision and candidate genes under selection in North American gray wolves

Rena M. Schweizer, Bridgett M. VonHoldt, Ryan Harrigan, James C. Knowles, Marco Musiani, David Coltman, John Novembre & Robert K. Wayne
Previous genetic studies of the highly mobile gray wolf (Canis lupus) found population structure that coincides with habitat and phenotype differences. We hypothesized that these ecologically distinct populations (ecotypes) should exhibit signatures of selection in genes related to morphology, coat color, and metabolism. To test these predictions, we quantified population structure related to habitat using a genotyping array to assess variation in 42,036 SNPs in 111 North American gray wolves. Using these SNP data and...

Data from: An indexed, mapped mutant library enables reverse genetics studies of biological processes in Chlamydomonas reinhardtii

Xiaobo Li, Ru Zhang, Weronika Patena, Spencer S. Gang, Sean R. Blum, Nina Ivanova, Rebecca Yue, Jacob M. Robertson, Paul A. Lefebvre, Sorel T. Fitz-Gibbon, Arthur R. Grossman & Martin C. Jonikas
The green alga Chlamydomonas reinhardtii is a leading single-celled model for dissecting biological processes in photosynthetic eukaryotes. However, its usefulness has been limited by difficulties in obtaining mutants in genes of interest. To allow generation of large numbers of mapped mutants, we developed high-throughput methods which: (1) Enable easy propagation on agar and cryogenic maintenance of tens of thousands of C. reinhardtii strains; (2) Identify mutant insertion sites and physical coordinates in such collections; (3)...

Data from: Chlamydomonas genome resource for laboratory strains reveals a mosaic of sequence variation, identifies true strain histories, and enables strain-specific studies

Sean D. Gallaher, Sorel T. Fitz-Gibbon, Anne G. Glaesener, Matteo Pellegrini & Sabeeha S. Merchant
Chlamydomonas reinhardtii is a widely used reference organism in studies of photosynthesis, cilia, and biofuels. Most research in this field uses a few dozen standard laboratory strains that are reported to share a common ancestry, but exhibit substantial phenotypic differences. In order to facilitate ongoing Chlamydomonas research and explain the phenotypic variation, we mapped the genetic diversity within these strains using whole-genome resequencing. We identified 524,640 single nucleotide variants and 4812 structural variants among 39...

Data from: Evolutionary and demographic history of the Californian scrub white oak species complex: an integrative approach

Joaquin Ortego, Victor Noguerales, Paul F. Gugger & Victoria L. Sork
Understanding the factors promoting species formation is a major task in evolutionary research. Here, we employ an integrative approach to study the evolutionary history of the Californian scrub white oak species complex (genus Quercus). To infer the relative importance of geographical isolation and ecological divergence in driving the speciation process, we (i) analyzed inter- and intra-specific patterns of genetic differentiation and employed an approximate Bayesian computation (ABC) framework to evaluate different plausible scenarios of species...

Data from: Agonistic reciprocity is associated with reduced male reproductive success within haremic social networks

Tessa K. Solomon-Lane, Devaleena S. Pradhan, Madelyne C. Willis & Matthew S. Grober
While individual variation in social behaviour is ubiquitous and causes social groups to differ in structure, how these structural differences affect fitness remains largely unknown. We used social network analysis of replicate bluebanded goby (Lythrypnus dalli) harems to identify the reproductive correlates of social network structure. In stable groups, we quantified agonistic behaviour, reproduction and steroid hormones, which can both affect and respond to social/reproductive cues. We identified distinct, optimal social structures associated with different...

Data from: Prevalence of coronary artery disease evaluated by coronary CT angiography in women with mammographically detected breast arterial calcifications

Leila Mostafavi, Wanda Marfori, Cesar Arellano, Alessia Tognolini, William Speier, Ali Adibi & Stefan G. Ruehm
To assess the correlation between breast arterial calcifications (BAC) on digital mammography and the extent of coronary artery disease (CAD) diagnosed with dual source coronary computed tomography angiography (CTA) in a population of women both symptomatic and asymptomatic for coronary artery disease. 100 consecutive women (aged 34 – 86 years) who underwent both coronary CTA and digital mammography were included in the study. Health records were reviewed to determine the presence of cardiovascular risk factors...

Registration Year

  • 2015
    25

Resource Types

  • Dataset
    25

Affiliations

  • University of California Los Angeles
    25
  • Princeton University
    2
  • University of California System
    2
  • Dominican University
    2
  • University of Chicago
    2
  • University of California, Santa Cruz
    2
  • Max Planck Institute for Ornithology
    1
  • National Institute of Infectious Diseases
    1
  • Estación Biológica de Doñana
    1
  • University of Massachusetts Amherst
    1