45 Works

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: 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: 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: 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: 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: 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: 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: 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...

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: 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: 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: Effects of nitrogen deposition on reproduction in a masting tree: benefits of higher seed production are trumped by negative biotic interactions

Michal Bogdziewicz, Elizabeth E. Crone, Michael A. Steele & Rafał Zwolak
Relatively little is known about the effects of anthropogenic environmental changes on reproductive ecology of trees. Yet, recruitment is a primary determinant of the long-term dynamics of plant populations in changing environments. We used the Long-Term Ecological Research site at Harvard Forest to evaluate the effects of chronic (over 25 years) nitrogen fertilization on reproductive ecology of red oaks (Quercus rubra). Oaks growing in fertilized plots produced 4–9 times more acorns than control trees. However,...

Data from: Sentinel cells, symbiotic bacteria, and toxin resistance in the social amoeba Dictyostelium discoideum

Debra A. Brock, William Éamon Callison, Joan E. Strassmann & David C. Queller
The social amoeba Dictyostelium discoideum is unusual among eukaryotes in having both unicellular and multicellular stages. In the multicellular stage, some cells, called sentinels, ingest toxins, waste, and bacteria. The sentinel cells ultimately fall away from the back of the migrating slug, thus removing these substances from the slug. However, some D. discoideum clones called farmers carry commensal bacteria through the multicellular stage while others called non-farmers do not. Farmers profit from their beneficial bacteria....

Data from: Atmospheric deposition exposes Qinling pandas to toxic pollutants

Yi-Ping Chen, Ying-Juan Zheng, Qiang Liu, Yi Song, Zhi-Sheng An, Qing-Yi Ma & Aaron M. Ellison
The giant panda (Ailuropoda melanoleuca) is one of the most endangered animals in the world, and it is recognized worldwide as a symbol for conservation. A previous study showed that wild and captive pandas, especially those of the Qinling subspecies, were exposed to toxicants in their diet of bamboo; the ultimate origin of these toxicants is unknown. Here we show that atmospheric deposition is the most likely origin of heavy metals and persistent organic pollutants...

Data from: Beyond animals and plants: dynamic maternal effects in the fungus Neurospora crassa

Kolea C. K. Zimmerman, Daniel A. Levitis & Anne Pringle
Maternal effects are widely documented in animals and plants, but not in fungi or other eukaryotes. A principal cause of maternal effects is asymmetrical parental investment in a zygote, creating greater maternal versus paternal influence on offspring phenotypes. Asymmetrical investments are not limited to animals and plants, but are also prevalent in fungi and groups including apicomplexans, dinoflagellates, and red algae. Evidence suggesting maternal effects among fungi is sparse and anecdotal. In an experiment designed...

Data from: Innovation in the collective brain

Michael Muthukrishna & Joseph Henrich
Innovation is often assumed to be the work of a talented few, whose products are passed on to the masses. Here, we argue that innovations are instead an emergent property of our species' cultural learning abilities, applied within our societies and social networks. Our societies and social networks act as collective brains. We outline how many human brains, which evolved primarily for the acquisition of culture, together beget a collective brain. Within these collective brains,...

Data from: Modelling tooth–prey interactions in sharks: the importance of dynamic testing

Katherine A. Corn, Stacy C. Farina, Jeffrey Brash & Adam P. Summers
The shape of shark teeth varies among species, but traditional testing protocols have revealed no predictive relationship between shark tooth morphology and performance. We developed a dynamic testing device to quantify cutting performance of teeth. We mimicked head-shaking behaviour in feeding large sharks by attaching teeth to the blade of a reciprocating power saw fixed in a custom-built frame. We tested three tooth types at biologically relevant speeds and found differences in tooth cutting ability...

Data from: Spontaneous metacognition in rhesus monkeys

Alexandra G. Rosati & Laurie R. Santos
Metacognition is the ability to think about thinking. Although monitoring and controlling one's knowledge is a key feature of human cognition, its evolutionary origins are debated. In the current study, we examined whether rhesus monkeys (Macaca mulatta; N = 120) could make metacognitive inferences in a one-shot decision. Each monkey experienced one of four conditions, observing a human appearing to hide a food reward in an apparatus consisting of either one or two tubes. The...

Data from: New insights on equid locomotor evolution from the lumbar region of fossil horses

Katrina Elizabeth Jones
The specialization of equid limbs for cursoriality is a classic case of adaptive evolution, but the role of the axial skeleton in this famous transition is not well understood. Extant horses are extremely fast and efficient runners, which use a stiff-backed gallop with reduced bending of the lumbar region relative to other mammals. This study tests the hypothesis that stiff-backed running in horses evolved in response to evolutionary increases in body size by examining lumbar...

Registration Year

  • 2016
    45

Resource Types

  • Dataset
    45

Affiliations

  • Harvard University
    45
  • University of Toronto
    3
  • Yale University
    3
  • Harvard Medical School
    3
  • University of Washington
    2
  • InterAmerican University of Puerto Rico
    2
  • Oregon State University
    2
  • University of North Carolina
    2
  • University of Wisconsin-Madison
    2
  • Pontifical Catholic University of Peru
    1