45 Works

Data from: Dispersal largely explains the Gondwanan distribution of the ancient tropical clusioid plant clade

Brad R. Ruhfel, Claudia P. Bove, C. Thomas Philbrick & Charles C. Davis
PREMISE OF THE STUDY: The clusioid clade (Malpighiales) has an ancient fossil record (∼90 Ma) and extant representatives exhibit a pantropical distribution represented on all former Gondwanan landmasses (Africa, Australia, India, Madagascar, and South America) except Antarctica. Several biogeographers have hypothesized that the clusioid distribution is an example of Gondwanan vicariance. Our aim is to test the hypothesis that the modern distribution of the clusioid clade is largely explained by Gondwanan fragmentation. METHODS: Using a...

Data from: Mutation is a sufficient and robust predictor of genetic variation for mitotic spindle traits in Caenorhabditis elegans

Reza Farhadifar, Jose Miguel Ponciano, Erik C. Andersen, Daniel J. Needleman & Charles F. Baer
Different types of phenotypic traits consistently exhibit different levels of genetic variation in natural populations. There are two potential explanations: either mutation produces genetic variation at different rates, or natural selection removes or promotes genetic variation at different rates. Whether mutation or selection is of greater general importance is a longstanding unresolved question in evolutionary genetics. We report mutational variances (VM) for 19 traits related to the first mitotic cell division in C. elegans, and...

Data from: Patterns and limitations of urban human mobility resilience under the influence of multiple types of natural disaster

Qi Wang & John E. Taylor
Natural disasters pose serious threats to large urban areas, therefore understanding and predicting human movements is critical for evaluating a population’s vulnerability and resilience and developing plans for disaster evacuation, response and relief. However, only limited research has been conducted into the effect of natural disasters on human mobility. This study examines how natural disasters influence human mobility patterns in urban populations using individuals’ movement data collected from Twitter. We selected fifteen destructive cases across...

Data from: Exploring phylogenetic relationships within Myriapoda and the effects of matrix composition and occupancy on phylogenomic reconstruction

Rosa Fernández, Gregory D. Edgecombe & Gonzalo Giribet
Myriapods, including the diverse and familiar centipedes and millipedes, are one of the dominant terrestrial arthropod groups. Although molecular evidence has shown that Myriapoda is monophyletic, its internal phylogeny remains contentious and understudied, especially when compared to those of Chelicerata and Hexapoda. Until now, efforts have focused on taxon sampling (e.g., by including a handful of genes from many species) or on maximizing matrix size (e.g., by including hundreds or thousands of genes in just...

Data from: Ancient mitochondrial DNA provides high-resolution time scale of the peopling of the Americas

Bastien Llamas, Lars Fehren-Schmitz, Guido Valverde, Julien Soubrier, Swapan Mallick, Nadin Rohland, Susanne Nordenfelt, Cristina Valdiosera, Stephen M. Richards, Adam Rohrlach, Maria Inés Barreto Romero, Isabel Flores Espinoza, Elsa Tomasto Cagigao, Lucía Watson Jiménez, Krzysztof Makowski, Ilán Santiago Leboreiro Reyna, Josefina Mansilla Lory, Julio Alejandro Ballivián Torrez, Mario A. Rivera, Richard L. Burger, Maria Constanza Ceruti, Johan Reinhard, R. Spencer Wells, Gustavo Politis, Calogero M. Santoro … & Wolfgang Haak
The exact timing, route, and process of the initial peopling of the Americas remains uncertain despite much research. Archaeological evidence indicates the presence of humans as far as southern Chile by 14.6 thousand years ago (ka), shortly after the Pleistocene ice sheets blocking access from eastern Beringia began to retreat. Genetic estimates of the timing and route of entry have been constrained by the lack of suitable calibration points and low genetic diversity of Native...

Data from: The role of isoforms in the evolution of cryptic coloration in Peromyscus mice

Ricardo Mallarino, Tess A. Linden, Catherine R. Linnen & Hopi E. Hoekstra
A central goal of evolutionary biology is to understand the molecular mechanisms underlying phenotypic adaptation. While the contribution of protein-coding and cis-regulatory mutations to adaptive traits has been well documented, additional sources of variation – such as the production of alternative RNA transcripts from a single gene, or isoforms – have been understudied. Here, we focus on the pigmentation gene Agouti, known to express multiple alternative transcripts, to investigate the role of isoform usage in...

Data from: Ant and mite diversity drives toxin variation in the Little Devil poison frog

Jenna R. McGugan, Gary D. Bryd, Alexandre B. Roland, Stephanie N. Caty, Nisha Kabir, Elicio E. Tapia, Sunia A. Trauger, Luis A. Coloma, Lauren A. O'Connell & Gary D. Byrd
Poison frogs sequester chemical defenses from arthropod prey, although the details of how arthropod diversity contributes to variation in poison frog toxins remains unclear. We characterized skin alkaloid profiles in the Little Devil poison frog, Oophaga sylvatica (Dendrobatidae), across three populations in northwestern Ecuador. Using gas chromatography/mass spectrometry, we identified histrionicotoxins, 3,5- and 5,8-disubstituted indolizidines, decahydroquinolines, and lehmizidines as the primary alkaloid toxins in these O. sylvatica populations. Frog skin alkaloid composition varied along a...

Data from: Does ecological specialization transcend scale? Habitat partitioning among individuals and species of Anolis lizards

Ambika Kamath & Jonathan B. Losos
Ecological specialization is common across all levels of biological organization, raising the question of whether the evolution of specialization at one scale in a taxon is linked to specialization at other scales. Anolis lizards have diversified repeatedly along axes of habitat use, but it remains unknown if this diversification into habitat use specialists is underlain by individual specialization. From repeated observations of individuals in a population of Anolis sagrei in Florida, we show that the...

Data from: A collection of non-human primate computed tomography scans housed in MorphoSource, a repository for 3D data

Lynn E. Copes, Lynn M. Lucas, James D. Thostenson, Hopi E. Hoekstra & Douglas M. Boyer
A dataset of high-resolution microCT scans of primate skulls (crania and mandibles) and certain postcranial elements was collected to address questions about primate skull morphology. The sample consists of 489 scans taken from 431 specimens, representing 53 species of most Primate families. These data have transformative reuse potential as such datasets are necessary for conducting high power research into primate evolution, but require significant time and funding to collect. Similar datasets were previously only available...

Data from: Ecological specialization and morphological diversification in Greater Antillean boas

Robert G. Reynolds, David C. Collar, Stesha A. Pasachnik, Matthew L. Niemiller, Alberto R. Puente-Rolon & Liam J. Revell
Colonization of islands can dramatically influence the evolutionary trajectories of organisms, with both deterministic and stochastic processes driving adaptation and diversification. Some island colonists evolve extremely large or small body sizes, presumably in response to unique ecological circumstances present on islands. One example of this phenomenon, the Greater Antillean boas, includes both small (<90 cm) and large (4 m) species occurring on the Greater Antilles and Bahamas, with some islands supporting pairs or trios of...

Data from: Correlated evolution of body and fin morphology in the cichlid fishes

Kara L. Feilich
Body and fin shape are chief determinants of swimming performance in fishes. Different configurations of body and fin shape can suit different locomotor specializations. The success of any configuration is dependent upon the hydrodynamic interactions between body and fins. Despite the importance of body-fin interactions for swimming, there are few data indicating whether body and fin configurations evolve in concert, or whether these structures vary independently. The cichlid fishes are a diverse family whose well-studied...

Data from: Foraging at the edge of the world: low‐altitude, high‐speed maneuvering in barn swallows

Douglas R. Warrick, Tyson L. Hedrick, Andrew A. Biewener, Kristen E. Crandell & Bret W. Tobalske
While prior studies of swallow manoeuvering have focused on slow-speed flight and obstacle avoidance in still air, swallows survive by foraging at high speeds in windy environments. Recent advances in field-portable, high-speed video systems, coupled with precise anemometry, permit measures of high-speed aerial performance of birds in a natural state. We undertook the present study to test: (i) the manner in which barn swallows (Hirundo rustica) may exploit wind dynamics and ground effect while foraging...

Data from: How chimpanzees integrate sensory information to select figs

Nathaniel J. Dominy, Justin D. Yeakel, Uttam Bhat, Lawrence Ramsden, Richard W. Wrangham & Peter W. Lucas
Figs are keystone resources that sustain chimpanzees when preferred fruits are scarce. Many figs retain a green(ish) colour throughout development, a pattern that causes chimpanzees to evaluate edibility on the basis of achromatic accessory cues. Such behaviour is conspicuous because it entails a succession of discrete sensory assessments, including the deliberate palpation of individual figs, a task that requires advanced visuomotor control. These actions are strongly suggestive of domain-specific information processing and decision-making, and they...

Data from: Biodiversity as a multidimensional construct: a review, framework and case study of herbivory's impact on plant biodiversity

S. Naeem, Case Prager, Brian Weeks, Alex Varga, Dan F.B. Flynn, Kevin Griffin, Robert Muscarella, Matthew Palmer, Stephen Wood, William Schuster & Dan F. B. Flynn
Biodiversity is inherently multidimensional, encompassing taxonomic, functional, phylogenetic, genetic, landscape and many other elements of variability of life on the Earth. However, this fundamental principle of multidimensionality is rarely applied in research aimed at understanding biodiversity's value to ecosystem functions and the services they provide. This oversight means that our current understanding of the ecological and environmental consequences of biodiversity loss is limited primarily to what unidimensional studies have revealed. To address this issue, we...

Data from: Optimal frequency of rabies vaccination campaigns in Sub-Saharan Africa

Alyssa M. Bilinski, Meagan C. Fitzpatrick, Charles E. Rupprecht, A. David Paltiel & Alison P. Galvani
Rabies causes more than 24 000 human deaths annually in Sub-Saharan Africa. The World Health Organization recommends annual canine vaccination campaigns with at least 70% coverage to control the disease. While previous studies have considered optimal coverage of animal rabies vaccination, variation in the frequency of vaccination campaigns has not been explored. To evaluate the cost-effectiveness of rabies canine vaccination campaigns at varying coverage and frequency, we parametrized a rabies virus transmission model to two...

Data from: Whole organism lineage tracing by combinatorial and cumulative genome editing

Aaron McKenna, Gregory M. Findlay, James A. Gagnon, Marshall S. Horwitz, Alexander Franz Schier & Jay Shendure
Multicellular systems develop from single cells through distinct lineages. However, current lineage-tracing approaches scale poorly to whole, complex organisms. Here, we use genome editing to progressively introduce and accumulate diverse mutations in a DNA barcode over multiple rounds of cell division. The barcode, an array of clustered regularly interspaced short palindromic repeats (CRISPR)/Cas9 target sites, marks cells and enables the elucidation of lineage relationships via the patterns of mutations shared between cells. In cell culture...

Data from: Leaf development and demography explain photosynthetic seasonality in Amazon evergreen forests

Jin Wu, Loren P. Albert, Aline P. Lopes, Natalia Restrepo-Coupe, Matthew Hayek, Kenia T. Wiedemann, Kaiyu Guan, Scott C. Stark, Bradley Christoffersen, Neill Prohaska, Julia V. Tavares, Suelen Marostica, Hideki Kobayashi, Mauricio L. Ferreira, Kleber Silva Campos, Rodrigo Da Silva, Paulo M. Brando, Dennis G. Dye, Travis E. Huxman, Alfredo R. Huete, Bruce W. Nelson & Scott R. Saleska
In evergreen tropical forests, the extent, magnitude, and controls on photosynthetic seasonality are poorly resolved and inadequately represented in Earth system models. Combining camera observations with ecosystem carbon dioxide fluxes at forests across rainfall gradients in Amazônia, we show that aggregate canopy phenology, not seasonality of climate drivers, is the primary cause of photosynthetic seasonality in these forests. Specifically, synchronization of new leaf growth with dry season litterfall shifts canopy composition toward younger, more light-use...

Data from: Phenotypic shifts in urban areas in the tropical lizard Anolis cristatellus

Kristin M. Winchell, Robert Graham Reynolds, Sofia R. Prado-Irwin, Alberto R. Puente-Rolón & Liam J. Revell
Urbanization is an important dimension of global change, and urban areas impose significant natural selection on species within them. Although many species persist in urban areas, little research has investigated whether populations have adapted to urbanization. Even less work has considered tropical regions, which have recently experienced dramatic urban growth. In the present study we focused on the neotropical lizard, Anolis cristatellus. We tested whether lizard ecology and morphology differ between urban and natural areas...

Data from: Closing a gap in tropical forest biomass estimation: taking crown mass variation into account in pantropical allometries

Pierre Ploton, Nicholas Barbier, Stéphane Takoudjou Momo, Maxime Réjou-Méchain, Faustin Boyemba Bosela, Georges Chuyong, Gilles Dauby, Vincent Droissart, Adeline Fayolle, Rosa Calisto Goodman, Mathieu Henry, Narcisse Guy Kamdem, John Katembo Mukirania, David Kenfack, Moses Libalah, Alfred Ngomanda, Vivien Rossi, Bonaventure Sonké, Nicolas Texier, Duncan Thomas, Donatien Zebaze, Pierre Couteron, Uta Berger & Raphaël Pélissier
Accurately monitoring tropical forest carbon stocks is an outstanding challenge. Allometric models that consider tree diameter, height and wood density as predictors are currently used in most tropical forest carbon studies. In particular, a pantropical biomass model has been widely used for approximately a decade, and its most recent version will certainly constitute a reference in the coming years. However, this reference model shows a systematic bias for the largest trees. Because large trees are...

Data from: Collective strategy for obstacle navigation during cooperative transport by ants

Helen F. McCreery, Zachary A. Dix, Michael D. Breed & Radhika Nagpal
Group cohesion and consensus have primarily been studied in the context of discrete decisions, but some group tasks require making serial decisions that build on one another. We examine such collective problem solving by studying obstacle navigation during cooperative transport in ants. In cooperative transport, ants work together to move a large object back to their nest. We blocked cooperative transport groups of Paratrechina longicornis with obstacles of varying complexity, analyzing groups' trajectories to infer...

Data from: Urban warming reduces aboveground carbon storage

Emily Meineke, Elsa Youngsteadt, Robert R. Dunn & Steven D. Frank
A substantial amount of global carbon is stored in mature trees. However, no experiments to date test how warming affects mature tree carbon storage. Using a unique, citywide, factorial experiment, we investigated how warming and insect herbivory affected physiological function and carbon sequestration (carbon stored per year) of mature trees. Urban warming increased herbivorous arthropod abundance on trees, but these herbivores had negligible effects on tree carbon sequestration. Instead, urban warming was associated with an...

Data from: Reconstruction of genetically identified neurons imaged by serial-section electron microscopy

Maximilian Joesch, David Mankus, Masahito Yamagata, Ali Shahbazi, Richard Shalek, Adi Suissa-Peleg, Markus Meister, Jeff W. Lichtman, Walter J. Scheirer, Joshua R. Sanes & Richard Schalek
Resolving patterns of synaptic connectivity in neural circuits currently requires serial section electron microscopy. However, complete circuit reconstruction is prohibitively slow and may not be necessary for many purposes such as comparing neuronal structure and connectivity among multiple animals. Here, we present an alternative strategy, targeted reconstruction of specific neuronal types. We used viral vectors to deliver peroxidase derivatives, which catalyze production of an electron-dense tracer, to genetically identified neurons, and developed a protocol that...

Data from: Horizontal gene acquisitions, mobile element proliferation, and genome decay in the host - restricted plant pathogen Erwinia tracheiphila

Lori R. Shapiro, Erin D. Scully, Timothy J. Straub, Jihye Park, Andrew G. Stephenson, Gwyn A. Beattie, Mark L. Gleason, Roberto Kolter, Miguel C. Coelho, Consuelo M. De Moraes, Mark C. Mescher & Olga Zhaxybayeva
Modern industrial agriculture depends on high density cultivation of genetically similar crop plants, creating favorable conditions for the emergence of novel pathogens with increased fitness in managed compared to ecologically intact settings. Here, we present the genome sequence of six strains of the cucurbit bacterial wilt pathogen Erwinia tracheiphila (Enterobacteriaceae) isolated from infected squash plants in New York, Pennsylvania, Kentucky, and Michigan. These genomes exhibit a high proportion of recent horizontal gene acquisitions, invasion and...

Data from: Comparative tests of the role of dewlap size in Anolis lizard speciation

Travis Ingram, Alexis Harrison, D. Luke Mahler, María Del Rosario Castañeda, Richard E. Glor, Anthony Herrel, Yoel E. Stuart & Jonathan B. Losos
Phenotypic traits may be linked to speciation in two distinct ways: character values may influence the rate of speciation or diversification in the trait may be associated with speciation events. Traits involved in signal transmission, such as the dewlap of Anolis lizards, are often involved in the speciation process. The dewlap is an important visual signal with roles in species recognition and sexual selection, and dewlaps vary among species in relative size as well as...

Data from: Life cycle matters: DNA barcoding reveals contrasting community structure between fern sporophytes and gametophytes

Joel H. Nitta, Jean-Yves Meyer, Ravahere Taputuarai & Charles C. Davis
Ferns are the only major lineage of vascular plants that have nutritionally independent sporophyte (diploid) and gametophyte (haploid) life stages. However, the implications of this unique life cycle for fern community ecology have rarely been considered. To compare patterns of community structure between fern sporophytes and gametophytes, we conducted a survey of the ferns of the islands of Moorea and Tahiti (French Polynesia). We first constructed a DNA barcode library (plastid rbcL and trnH–psbA) for...

Registration Year

  • 2016

Resource Types

  • Dataset


  • Harvard University
  • University of Toronto
  • Yale University
  • Harvard Medical School
  • University of Washington
  • InterAmerican University of Puerto Rico
  • Oregon State University
  • University of North Carolina
  • University of Wisconsin-Madison
  • Pontifical Catholic University of Peru