46 Works

Data from: Targeted sequencing of venom genes from cone snail genomes improves understanding of conotoxin molecular evolution

Mark A. Phuong & Gusti N. Mahardika
To expand our capacity to discover venom sequences from the genomes of venomous organisms, we applied targeted sequencing techniques to selectively recover venom gene superfamilies and non-toxin loci from the genomes of 32 cone snail species (family, Conidae), a diverse group of marine gastropods that capture their prey using a cocktail of neurotoxic peptides (conotoxins). We were able to successfully recover conotoxin gene superfamilies across all species with high confidence (> 100X coverage) and used...

Data from: Genome-wide expression reveals multiple systemic effects associated with detection of anticoagulant poisons in bobcats (Lynx rufus)

Devaughn Fraser, Alice Mouton, Laurel E.K. Serieys, Steve Cole, Scott Carver, Sue Vandewoude, Michael Lappin, Seth P.D. Riley, Robert Wayne & Laurel E. K. Serieys
Anticoagulant rodenticides (ARs) are indiscriminate toxicants that threaten non-target predatory and scavenger species through secondary poisoning. Accumulating evidence suggests that AR exposure may have disruptive sublethal consequences on individuals that can affect fitness. We evaluated AR-related effects on genome wide expression patterns in a population of bobcats in southern California. We identify differential expression of genes involved in xenobiotic metabolism, endoplasmic reticulum stress response, epithelial integrity, and both adaptive and innate immune function. Further, we...

Data from: Fossil lemurs from Egypt and Kenya suggest an African origin for Madagascar’s aye-aye

Gregg F. Gunnell, Doug M. Boyer, Anthony F. Friscia, Steven Heritage, Fredrick K. Manthi, Ellen R. Miller, Hesham M. Sallam, Nancy B. Simmons, Nancy J. Stevens & Erik R. Seiffert
In 1967 G.G. Simpson described three partial mandibles from early Miocene deposits in Kenya that he interpreted as belonging to a new strepsirrhine primate, Propotto. This interpretation was quickly challenged, with the assertion that Propotto was not a primate, but rather a pteropodid fruit bat. The latter interpretation has not been questioned for almost half a century. Here we re-evaluate the affinities of Propotto, drawing upon diverse lines of evidence to establish that this strange...

Data from: Landscape genomics provides evidence of climate-associated genetic variation in Mexican populations of Quercus rugosa Nee

Karina Martins, Paul Gugger, Jesus Llanderal-Mendoza, Antonio González-Rodríguez, Sorel T. Fitz-Gibbon, Jian-Li Zhao, Hernando Rodríguez-Correa, Ken Oyama, Victoria L. Sork & Paul F. Gugger
Local adaptation is a critical evolutionary process that allows plants to grow better in their local compared to nonnative habitat and results in species-wide geographic patterns of adaptive genetic variation. For forest tree species with a long generation time, this spatial genetic heterogeneity can shape the ability of trees to respond to rapid climate change. Here, we identify genomic variation that may confer local environmental adaptations and then predict the extent of adaptive mismatch under...

Data from: Give the machine a hand: a Boolean time-based decision-tree template for rapidly finding animal behaviours in multi-sensor data

Rory P. Wilson, Mark D. Holton, Agustina Di Virgilio, Hannah Williams, Emily L. C. Shepard, Sergio Lambertucci, Flavio Quintana, Juan E Sala, Bharathan Balaji, Eun Sun Lee, Mani Srivastava, D. Michael Scantlebury & Carlos M. Duarte
1. The development of multi-sensor animal-attached tags, recording data at high frequencies, has enormous potential in allowing us to define animal behaviour. 2. The high volumes of data, are pushing us towards machine-learning as a powerful option for distilling out behaviours. However, with increasing parallel lines of data, systems become more likely to become processor limited and thereby take appreciable amounts of time to resolve behaviours. 3. We suggest a Boolean approach whereby critical changes...

Data from: Genetic control of seed shattering during African rice domestication

Shuwei Lv, Wenguang Wu, Muhua Wang, Rachel S. Meyer, Marie-Noelle Ndjiondjop, Lubin Tan, Haiying Zhou, Jianwei Zhang, Yongcai Fu, Hongwei Cai, Chuanqing Sun, Rod A. Wing & Zuofeng Zhu
Domestication represents a unique opportunity to study the evolutionary process. The elimination of seed dispersal traits was a key step in the evolution of cereal crops under domestication. Here, we show that ObSH3, a YABBY transcription factor, is required for the development of the seed abscission layer. Moreover, selecting a genomic segment deletion containing SH3 resulted in the loss of seed dispersal in populations of African cultivated rice (Oryza glaberrima Steud.). Functional characterization of SH3...

Data from: Counting crows: flock structure and subgroup size variation in an urban population of crows

Florian Uhl, Max Ringler, Rachael Miller, Sarah A. Deventer, Thomas Bugnyar & Christine Schwab
Social complexity arises from the formation of social relationships like social bonds and dominance hierarchies. In turn, these aspects may be affected by the degree of fission-fusion dynamics, i.e. changes in group size and composition over time. Whilst fission-fusion dynamics has been studied in mammals, birds have received comparably little attention, despite some species having equally complex social lives. Here, we investigated the influence of environmental factors on aspects of fission-fusion dynamics in a free-ranging...

Data from: Social interactions shape individual and collective personality in social spiders

Edmund R. Hunt, Brian Mi, Camila Fernandez, Brandyn M. Wong, Jonathan N. Pruitt & Noa Pinter-Wollman
The behavioural composition of a group and the dynamics of social interactions can both influence how social animals work collectively. For example, individuals exhibiting certain behavioural tendencies may have a disproportionately large impact on the group, and so are referred to as keystone individuals, while interactions between individuals can facilitate information transmission about resources. Despite the potential impact of both behavioural composition and interactions on collective behaviour, the relationship between consistent behaviours, also known as...

Data from: Anisotropic growth is achieved through the additive mechanical effect of material anisotropy and elastic asymmetry

Firas Bou Daher, Yuanjie Chen, Behruz Bozorg, Jack Clough, Henrik Jönsson & Siobhan A. Braybrook
Fast directional growth is a necessity for the young seedling; after germination, it needs to quickly penetrate the soil to begin its autotrophic life. In most dicot plants, this rapid escape is due to the anisotropic elongation of the hypocotyl, the columnar organ between the root and the shoot meristems. Anisotropic growth is common in plant organs and is canonically attributed to cell wall anisotropy produced by oriented cellulose fibers. Recently, a mechanism based on...

Data from: Of puzzles and pavements: a quantitative exploration of leaf epidermal cell shape

Róza V. Vőfély, Joseph Gallagher, Grace D. Pisano, Madelaine Bartlett & Siobhan A. Braybrook
Epidermal cells of leaves are diverse: tabular pavement cells, trichomes, and stomatal complexes. Pavement cells from the monocot Zea mays (maize) and the eudicot Arabidopsis thaliana (Arabidopsis) have highly undulate anticlinal walls. The molecular basis for generating these undulating margins has been extensively investigated in these species. This has led to two assumptions: first, that particular plant lineages are characterized by particular pavement cell shapes; and second, that undulatory cell shapes are common enough to...

Data from: Multifactorial processes underlie parallel opsin loss in neotropical bats

Alexa Sadier, Kalina T. J. Davies, Laurel R. Yohe, Kun Yun, Paul Donat, Brandon P. Hedrick, Elizabeth R. Dumont, Liliana M. Davalos, Stephen J. Rossiter & Karen E. Sears
The loss of previously adaptive traits is typically linked to relaxation in selection, yet the molecular steps leading to such repeated losses are rarely known. Molecular studies of loss have tended to focus on gene sequences alone, but overlooking other aspects of protein expression might underestimate phenotypic diversity. Insights based almost solely on opsin gene evolution, for instance, have made mammalian color vision a textbook example of phenotypic loss. We address this gap by investigating...

Data from: How sea-level change mediates genetic divergence in coastal species across regions with varying tectonic and sediment processes

Greer A. Dolby, Ryan A. Ellingson, Lloyd T. Findley & David K. Jacobs
Plate tectonics and sediment processes control regional continental shelf topography. We examine the genetic consequences of how glacial-associated sea-level change interacted with variable near-shore topography since the last glaciation. We reconstructed the size and distribution of areas suitable for tidal estuary formation from the Last Glacial Maximum, ~20 thousand years ago, to present from San Francisco, California, USA (~38 °N) to Reforma, Sinaloa, Mexico (~25 °N). We assessed range-wide genetic structure and diversity of three...

Data from: An extensive suite of functional traits distinguishes wet and dry Hawaiian forests and enables prediction of species vital rates

Camila D. Medeiros, Christine Scoffoni, Grace John, Megan Bartlett, Faith Inman-Narahari, Rebecca Ostertag, Susan Cordell, Christian Giardina, Lawren Sack, Megan K. Bartlett & Grace P. John
1. The application of functional traits to predict and explain plant species’ distributions and vital rates has been a major direction in functional ecology for decades, yet numerous physiological traits have not yet been incorporated into the approach. 2. Using commonly measured traits such as leaf mass per area (LMA) and wood density (WD), and additional traits related to water transport, gas exchange and resource economics, including leaf vein, stomatal, and wilting traits, we tested...

Data from: Contemporaneous radiations of fungi and plants linked to symbiosis

François Lutzoni, Michael D. Nowak, Michael E. Alfaro, Valérie Reeb, Jolanta Miadlikowska, Michael Krug, A. Elizabeth Arnold, Louise A. Lewis, David L. Swofford, David Hibbett, Khidir Hilu, Timothy Y. James, Dietmar Quandt & Susana Magallón
Interactions between fungi and plants, including parasitism, mutualism, and saprotrophy, have been invoked as key to their respective macroevolutionary success. Here we evaluate the origins of plant-fungal symbioses and saprotrophy using a time-calibrated phylogenetic framework that reveals linked and drastic shifts in diversification rates of each kingdom. Fungal colonization of land was associated with at least two origins of terrestrial green algae and preceded embryophytes (as evidenced by losses of fungal flagellum, ca. 720 Ma),...

Data from: Gene expression shifts in yellow-bellied marmots prior to natal dispersal

Tiffany C. Armenta, Steve W. Cole, Daniel H. Geschwind, Daniel T. Blumstein & Robert K. Wayne
The causes and consequences of vertebrate natal dispersal have been studied extensively, yet little is known about the molecular mechanisms involved. We used RNA-seq to quantify transcriptomic gene expression in blood of wild yellow-bellied marmots (Marmota flaviventer) prior to dispersing from or remaining philopatric to their natal colony. We tested three predictions. First, we hypothesized dispersers and residents will differentially express genes and gene networks since dispersal is physiologically demanding. Second, we expected differentially expressed...

Data from: Postconvulsive central apnea as a biomarker for sudden unexpected death in epilepsy (SUDEP)

Laura Vilella, Nuria Lacuey, Johnson P. Hampson, M.R. Sandhya Rani, Rup K. Sanju, Daniel Friedman, Maromi Nei, Kingman Strohl, Catherine Scott, Brian K. Gehlbach, Bilal Zony, Norma J. Hupp, Anita Zaremba, Nassim Shafiabadi, Xihue Zhao, Victoria Reick-Mitrisin, Stephan Schuele, Jennifer Ogren, Ronald M. Harper, Beate Diehl, Lisa Bateman, Orrin Devinsky, George B. Richerson, Philippe Ryvlin & Samden D. Lhatoo
Objective: To characterize peri-ictal apnea and post-ictal asystole in generalized convulsive seizures (GCS) of intractable epilepsy. Methods: Prospective, multi-center epilepsy monitoring study of autonomic and breathing biomarkers of SUDEP in patient’s ≥18 years old with intractable epilepsy and monitored GCS. Video EEG, thoraco-abdominal excursions, nasal airflow, capillary oxygen saturation and electrocardiography were analyzed. Results: We studied 148 GCS in 87 patients. Nineteen patients had generalized epilepsy, 65 had focal, one had both and in two,...

Data from: Evidence of host-associated divergence from coral-eating snails (genus Coralliophila) in the Coral Triangle

Sara E. Simmonds, Vincent Chou, Samantha H. Cheng, Rita Rachmawati, Hilconida P. Campulong, Paul H. Barber, Hilconida P. Calumpong & G. Ngurah Mahardika
We studied how host-associations and geography shape the genetic structure of sister species of marine snails Coralliophila radula (A. Adams, 1853) and C. violacea (Kiener, 1836). These obligate ectoparasites prey upon corals and are sympatric throughout much of their ranges in coral reefs of the tropical and subtropical Indo-Pacific. We tested for population genetic structure of snails in relation to geography and their host corals using mtDNA (COI) sequences in minimum spanning trees and AMOVAs....

Tree species abundance through time in tropical forest census plots, Panama

Richard Condit, Rolando Pérez, Salomón Aguilar, Suzanne Lao, Foster Robin & Stephen Hubbell
All trees at least 1 cm diameter at breast height were censused in three sites in Panama. The Barro Colorado plot is 50 hectares in area and was fully censused on eight occasions between 1982 and 2015. The Sherman plot is 5.96 hectares and was fully censuses four times between 1996 and 2009. The Cocoli plot is 4 hectares and was censused three times between 1994 and 1999. The three accompanying tables give the population...

Data from: Dietary specialization is linked to reduced species durations in North American fossil canids

Mairin Balisi, Corinna Casey & Blaire Van Valkenburgh
How traits influence species persistence is a fundamental question in ecology, evolution, and paleontology. We test the relationship between dietary traits and both species duration and locality coverage over 40 million years in North American canids, a clade with considerable ecomorphological disparity and a dense fossil record. Because ecomorphological generalization--broad resource use--may enable species to withstand disturbance, we predicted that canids of average size and mesocarnivory would exhibit longer durations and wider distributions than specialized...

Data from: Globally consistent impact of tropical cyclones on the structure of tropical and subtropical forests

Thomas Ibanez, Gunnar Keppel, Christophe Menkes, Thomas W. Gillespie, Matthieu Lengaigne, Morgan Mangeas, Gonzalo Rivas-Torres & Philippe Birnbaum
1. Tropical cyclones (TCs) are large-scale disturbances that regularly impact tropical forests. Although long-term impacts of TCs on forest structure have been proposed, a global test of the relationship between forest structure and TC frequency and intensity is lacking. We test on a pantropical scale whether TCs shape the structure of tropical and subtropical forests in the long-term. 2. We compiled forest structural features (stem density, basal area, mean canopy height and maximum tree size)...

Data from: Olfaction written in bone: cribriform plate size parallels olfactory receptor gene repertoires in Mammalia

Deborah J. Bird, William J. Murphy, Lester Fox-Rosales, Iman Hamid, Robert A. Eagle & Blaire Van Valkenburgh
The evolution of mammalian olfaction is manifested in a remarkable diversity of gene repertoires, neuroanatomy, and skull morphology across living species. Olfactory receptor genes (ORG), which initiate the conversion of odorant molecules into odor perceptions and help an animal resolve the olfactory world, range in number from a mere handful to several thousand genes across species. Within the snout, each of these ORGs is exclusively expressed by a discrete population of olfactory sensory neurons (OSN),...

Data from: Urbanization and anticoagulant poisons promote immune dysfunction in bobcats

Laurel E.K. Serieys, Amanda J. Lea, Marta Epeldegui, Tiffany C. Armenta, Joanne Moriarty, Sue Vandewoude, Scott Carver, Janet Foley, Robert K. Wayne, Seth P.D. Riley, Christel H. Uittenbogaart, Laurel E. K. Serieys & Seth P. D. Riley
Understanding how human activities influence immune response to environmental stressors can support biodiversity conservation across increasingly urbanizing landscapes. We studied a bobcat (Lynx rufus) population in urban southern California that experienced a rapid population decline from 2002–2005 due to notoedric mange. Because anticoagulant rodenticide (AR) exposure was an underlying complication in mange deaths, we aimed to understand sublethal contributions of urbanization and ARs on 65 biochemical markers of immune and organ function. Variance in immunological...

Data from: Optimists or realists? How ants allocate resources in making reproductive investments.

Brittany L. Enzmann & Peter Nonacs
1. Parents often face an investment trade-off between either producing many small or fewer large offspring. When environments vary predictably, the fittest parental solution matches available resources by varying only number of offspring and never optimal individual size. However when mismatches occur often between parental expectations and true resource levels, dynamic models like multifaceted parental investment (MFPI) and parental optimism (PO) both predict offspring size can vary significantly. MFPI is a “realist” strategy: parents assume...

Data from: Relatedness within and between leks of golden-collared manakin differ between sexes and age classes

Leonida Fusani, Julia Barske, Chiara Natali, Guido Chelazzi & Claudio Ciofi
Several hypotheses have been advanced to explain the evolution of leks, a mating system in which males aggregate at display sites where females choose their mates. Only a small proportion of males obtain copulations, and why other males join the lek remains unexplained. One hypothesis has called kin selection into play: if juvenile males join leks where their relatives display and contribute to attract females to the lek, they can gain indirect fitness benefits. We...

Data from: Resolving deep nodes in an ancient radiation of neotropical fishes in the presence of conflicting signals from incomplete lineage sorting

Fernando Alda, Victor A. Tagliacollo, Maxwell J. Bernt, Brandon T. Waltz, William B. Ludt, Brant C. Faircloth, Michael E. Alfaro, James S. Albert & Prosanta Chakrabarty
Resolving patterns of ancient and rapid diversifications is one of the most challenging tasks in evolutionary biology. These difficulties arise from confusing phylogenetic signals that are associated with the interplay of incomplete lineage sorting and homoplasy. Phylogenomic analyses of hundreds, or even thousands, of loci offer the potential to resolve such contentious relationships. Yet, how much useful phylogenetic information these large data sets contain remains uncertain and often goes untested. Here, we assess the utility...

Registration Year

  • 2018

Resource Types

  • Dataset
  • Text


  • University of California Los Angeles
  • Princeton University
  • University of Michigan-Ann Arbor
  • University of California System
  • Duke University
  • University of Cambridge
  • University of Sao Paulo
  • University of Vienna
  • Yale University
  • University of Antwerp