220 Works

Fragmentation reduces community-wide taxonomic and functional diversity of dispersed tree seeds in the Central Amazon

Elaine Hooper & Mark Ashton
The Amazon harbors one of the most diverse tree floras on earth, and most species depend on mutualists for pollination and seed dispersal. This makes them susceptible to reproductive decline in fragmented forest because many of these mutualists suffer area-related extinction in fragments. It remains unknown, however, whether this highly biodiverse tree flora will reproduce and ultimately persist in fragmented forest. We conducted a two-year study of seed-fall in an experimentallyfragmented, highly-diverse Central Amazonian forest....

Trophic rewilding revives biotic resistance to shrub invasion

Jennifer Guyton, Johan Pansu, Tyler Kartzinel, Tyler Coverdale, Arjun Potter, Joshua Daskin, Matthew Hutchinson, Ana Gledis Da Conceição, Mike Peel, Marc Stalmans & Robert Pringle
Trophic rewilding seeks to rehabilitate degraded ecosystems by repopulating them with large animals, thereby reestablishing strong top-down interactions. Yet there are vanishingly few tests of whether such initiatives can restore ecosystem structure and functions, and on what timescales. Here we show that war-induced collapse of large-mammal populations in Mozambique’s Gorongosa National Park exacerbated woody encroachment by the invasive shrub Mimosa pigra—one of the world’s ‘100 worst’ invasive species—and that one decade of concerted trophic rewilding...

Energy drinks consumption and perceptions among university students in Beirut, Lebanon: a mixed methods approach

Malake Ghozayel, Ali Ghaddar, Ghada Farhat, Lara Nasreddine, Janine Kara & Lamis Jomaa
Background: Energy drinks (ED) are caffeine and sugar-rich beverages with other ingredients that are marketed for their energy boosting and performance-enhancing effects. The consumption of these drinks, with and without alcohol, is dramatically increasing worldwide, despite the reported side effects and potential harms to consumers. Few studies, to date, have explored the perceptions and experiences of young adults towards these beverages. Objective: The present study aimed to explore the consumption patterns and correlates of ED...

The geographic distribution of the imperiled Barrens Darter, Etheostoma forbesi, and threats of hybridization with the closely related Fringed Darter, Etheostoma crossopterum.

Richard Harrington, Jeffrey Simmons & Thomas Near
The Barrens Darter, Etheostoma forbesi, is one of the most geographically restricted freshwater fish species in North America, with a distribution limited to headwater portions of nine streams in the western part of the upper Caney Fork, a tributary of the Cumberland River in Tennessee. This limited geographic distribution makes E. forbesi especially vulnerable to potential threats posed by human alterations to rivers and streams, and the risk of ecological competition and introgressive hybridization with...

Hierarchical multi-grain models improve descriptions of species’ environmental associations, distribution, and abundance

Katherine Mertes, Marta Jarzyna & Walter Jetz
The characterization of species’ environmental niches and spatial distribution predictions based on them are now central to much of ecology and conservation, but implicitly requires decisions about the appropriate spatial scale (i.e. grain) of analysis. Ecological theory and empirical evidence suggest that range-resident species respond to their environment at two characteristic, hierarchical spatial grains: (i) response grain, the (relatively fine) grain at which an individual uses environmental resources, and (ii) occupancy grain, the (relatively coarse)...

Functional consequences of phenotypic variation between locally adapted populations: swimming performance and ventilation in extremophile fish

Michael Tobler, Lenin Arias-Rodriguez & Henry Camarillo
Natural selection drives the evolution of traits to optimize organismal performance, but optimization of one aspect of performance can often influence other aspects of performance. Here, we asked how phenotypic variation between locally adapted fish populations affects locomotion and ventilation, testing for functional trade-offs and trait-performance correlations. Specifically, we investigated two populations of livebearing fish (Poecilia mexicana) that inhabit distinct habitat types (hydrogen-sulfide-rich springs and adjacent nonsulfidic streams). For each individual, we quantified different metrics...

Assessing the effects of elephant foraging on the structure and diversity of an Afrotropical forest

Cooper Rosin, Kendall Beals, Michael Belovitch, Ruby Harrison, Megan Pendred, Megan Sullivan, Nicolas Yao & John Poulsen
African forest elephants (Loxodonta cyclotis) are ecosystem engineers that browse and damage large quantities of vegetation during their foraging and movement. Though elephant trail networks and clearings are conspicuous features of many African forests, the consequences of elephant foraging for forest structure and diversity are poorly documented. In this study in northeastern Gabon, we compare stem size, stem density, proportional damage, species diversity, and species relative abundance of seedlings and saplings in the vicinity of...

The Role of Linguistic Features in Domain Adaptation: TAG Parsing of Questions

Aarohi Srivastava, Robert Frank, Sarah Widder & David Chartash

Data from: Three-dimensional soft tissue preservation revealed in the skin of a non-avian dinosaur

Matteo Fabbri, Jasmina Wiemann, Fabio Manucci & Derek E. G. Briggs
The most commonly preserved soft tissues associated with ornithischian dinosaurs are skin remains. The apparent resistance of hadrosaur skin to decay, and its abundance in the fossil record relative to that of other tetrapods, has been attributed to factors such as thickness and composition. Here we report additional intrinsic factors within hadrosaur skin: 3D‐preserved eumelanin‐bearing bodies, dermal cells and blood vessel fragments in an organic matrix composed of protein fossilization products. The skin is much...

Thinner bark increases sensitivity of wetter Amazonian tropical forests to fire

Ann Carla Staver, Paulo M. Brando, Jos Barlow, Douglas C. Morton, C.E. Timothy Paine, Yadvinder Malhi, Alejandro Araujo Murakami & Jhon Pasquel
Understory fires represent an accelerating threat to Amazonian tropical forests and can, during drought, affect larger areas than deforestation itself. These fires kill trees at rates varying from < 10 to c. 90% depending on fire intensity, forest disturbance history and tree functional traits. Here, we examine variation in bark thickness across the Amazon. Bark can protect trees from fires, but it is often assumed to be consistently thin across tropical forests. Here, we show...

Fruit syndromes in Viburnum: correlated evolution of color, nutritional content, and morphology in bird-dispersed fleshy fruits

Miranda Sinnott-Armstrong, Chong Lee, Wendy Clement & Michael Donoghue
Premise A key question in plant dispersal via animal vectors is where and why fruit colors vary between species and how color relates to other fruit traits. To better understand the factors shaping the evolution of fruit color diversity, we tested for the existence of syndromes of traits (color, morphology, and nutrition) in the fruits of Viburnum. We placed these results in a larger phylogenetic context and reconstructed ancestral states to assess how Viburnum fruit...

Restoration mediated secondary contact leads to introgression of alewife ecotypes separated by a colonial-era dam

Kerry Reid, John Carlos Garza, Eric Palkovacs, Steven Gephard, Adalgisa Caccone & David Post
Secondary contact may have important implications for ecological and evolutionary processes; however, few studies have tracked the outcomes of secondary contact from its onset in natural ecosystems. We evaluated an anadromous alewife (Alosa pseudoharengus) reintroduction project in Rogers Lake (Connecticut, USA), which contains a landlocked alewife population that was isolated as a result of colonial era damming. After access to the ocean was restored, adult anadromous alewife were stocked into the lake. We assessed anadromous...

Data from: Dispersal increases the resilience of tropical savanna and forest distributions

Nikunj Goel, Vishwesha Guttal, Simon Levin & Carla Staver
Global change may induce changes in savanna and forest distributions, but the dynamics of these changes remain unclear. Classical biome theory suggests that climate is predictive of biome distributions, such that shifts will be continuous and reversible. This view, however, cannot explain the overlap in the climatic ranges of tropical biomes, which some argue may result from fire-vegetation feedbacks, maintaining savanna and forest as bistable states. Under this view, biome shifts are argued to be...

Data from: Long-term dynamics of liana seedlings suggest decelerating increases in liana relative abundance over time

Maria Natalia Umaña, Eric Manzané-Pinzón & Liza Comita
Over the past decades, tropical forests have experienced both compositional and structural changes. In the Neotropics, researchers at multiple sites have observed significant increases in the abundance and biomass of lianas (i.e. woody vines) relative to trees. However, the role of dynamics at early life stages in contributing to increasing liana abundance remains unclear. We took advantage of a unique dataset on seedling dynamics over 16 years in ~20,000 1-m2plots in a tropical forest in...

Data from: Determinants of tree cover in tropical floodplains

Joshua H. Daskin, Filipe Aires & A. Carla Staver
In uplands, water availability and fire limit tree cover, differentiating between tropical forest, savanna, and grassland biomes. In contrast, we know less about tropical floodplain tree cover determinants, although these habitats similarly include near-treeless grasslands, moderately treed savannas, and forests. Using GIS and remotely sensed data from 13 large tropical and sub-tropical floodplain ecosystems on five continents, we show that floodplain tree cover increases with climatic water balance (= rainfall - potential evapotranspiration) and decreases...

Data from: A phylogenomic framework for pelagiarian fishes (Acanthomorpha: Percomorpha) highlights mosaic radiation in the open ocean

Matthew Friedman, Kara Feilich, Hermione Beckett, Michael Alfaro, Brant Faircloth, David Černý, Masaki Miya, Thomas Near & Richard Harrington
The fish clade Pelagiaria, which includes tunas as its most famous members, evolved remarkable morphological and ecological variety in a setting not generally considered conducive to diversification: the open ocean. Relationships within Pelagiaria have proven elusive due to short internodes subtending major lineages suggestive of rapid early divergences. Using a novel sequence dataset of over 1000 ultraconserved DNA elements (UCEs) for 94 of the 286 species of Pelagiaria (more than 70% of genera), we provide...

Data from: Resource acquisition strategies facilitate Gilbertiodendron dewevrei monodominance in African lowland forests

Jefferson Hall, David Harris, Kristin Saltonsall, Vincent Medjibe, Mark Ashton & Benjamin Turner
1. Tropical forests are hyperdiverse, yet extensive areas of monodominant forest occur in the tropics worldwide. Most long-lived and persistent monodominant tree species form ectomycorrhizal fungi symbioses, allowing them to obtain nutrients directly from soil organic matter. This might promote monodominance by reducing nutrient availability to co-occurring species, the majority of which form associations with arbuscular mycorrhizal fungi. 2. Gilbertiodendron dewevrei forest is the most widespread monodominant forest in tropical Africa. Its distribution appears determined...

Data from: Endocranial anatomy and life habits of the Early Triassic archosauriform Proterosuchus fergusi

Emily Brown, Richard Butler, Martin Ezcurra, Bhart-Anjan Bhullar & Stephan Lautenschlager
Proterosuchids are an important group of carnivorous basal archosauriforms characterised by a bizarre and enigmatic downturned premaxilla that overhangs the lower jaw. They are particularly significant because they radiated in the immediate aftermath of the Permian–Triassic mass extinction, and represent one of the best known ‘disaster taxa’ following that event. While traditionally considered semi-aquatic, recent histological studies and geological data have suggested that they more likely inhabited terrestrial environments. By utilising computed tomographic (CT) data,...

Inferring the mammal tree: Species-level sets of phylogenies for questions in ecology, evolution, and conservation

Nathan S. Upham, Jacob A. Esselstyn & Walter Jetz
Big, time-scaled phylogenies are fundamental to connecting evolutionary processes to modern biodiversity patterns. Yet inferring reliable phylogenetic trees for thousands of species involves numerous trade-offs that have limited their utility to comparative biologists. To establish a robust evolutionary timescale for all ~6000 living species of mammals, we developed credible sets of trees that capture root-to-tip uncertainty in topology and divergence times. Our ‘backbone-and-patch’ approach to tree-building applies a newly assembled 31-gene supermatrix to two levels...

Data from: Asymmetric ON-OFF processing of visual motion cancels variability induced by the structure of natural scenes

Juyue Chen, Holly B. Mandel, James E. Fitzgerald & Damon A. Clark
Animals detect motion using a variety of visual cues that reflect regularities in the natural world. Experiments in animals across phyla have shown that motion percepts incorporate both pairwise and triplet spatiotemporal correlations that could theoretically benefit motion computation. However, it remains unclear how visual systems assemble these cues to build accurate motion estimates. Here we use comprehensive measurements of fruit fly motion perception to show how flies combine local pairwise and triplet correlations to...

Data from: Molecular phylogenetics of squirrelfishes and soldierfishes (Teleostei:Beryciformes: Holocentridae): reconciling more than 100 years of taxonomic confusion

Alex Dornburg, Jon A. Moore, Rachel Webster, Dan L. Warren, Matthew C. Brandley, Teresa L. Iglesias, Peter C. Wainwright & Thomas J. Near
Squirrelfishes and soldierfishes (Holocentridae) are among the most conspicuous species in the nocturnal reef fish community. However, there is no clear consensus regarding their evolutionary relationships, which is reflected in a complicated taxonomic history. We collected DNA sequence data from multiple single copy nuclear genes and one mitochondrial gene sampled from over fifty percent of the recognized holocentrid species and infer the first species-level phylogeny of the Holocentridae. Our results strongly support the monophyly of...

Data from: Diffusion tensor imaging in patients with glioblastoma multiforme using the supertoroidal model

Choukri Mekkaoui, Philippe Metellus, William J. Kostis, Roberto Martuzzi, Fabricio R. Pereira, Jean-Paul Beregi, Timothy G. Reese, Todd R. Constable & Marcel P. Jackowski
Purpose: Diffusion Tensor Imaging (DTI) is a powerful imaging technique that has led to improvements in the diagnosis and prognosis of cerebral lesions and neurosurgical guidance for tumor resection. Traditional tensor modeling, however, has difficulties in differentiating tumor-infiltrated regions and peritumoral edema. Here, we describe the supertoroidal model, which incorporates an increase in surface genus and a continuum of toroidal shapes to improve upon the characterization of Glioblastoma multiforme (GBM). Materials and Methods: DTI brain...

Data from: Introgression between invasive and native blue mussels (genus Mytilus) in the central California hybrid zone.

Norah P. Saarman & Grant H. Pogson
The ecological and genetic factors determining the extent of introgression between species in secondary contact zones remain poorly understood. Here, we investigate the relative importance of isolating barriers and the demographic expansion of invasive Mytilus galloprovincialis on the magnitude and the direction of introgression with the native Mytilus trossulus in a hybrid zone in central California. We use double-digest restriction-site-associated DNA sequencing (ddRADseq) to genotype 1337 randomly selected single nucleotide polymorphisms and accurately distinguish early...

Data from: Understanding angiosperm diversification using small and large phylogenetic trees

Stephen A. Smith, Jeremy M. Beaulieu, Alexandros Stamatakis, Michael J. Donoghue, J. M. Beaulieu, M. J. Donoghue, S. A. Smith & A. Stamatakis
How will the emerging possibility of inferring ultra-large phylogenies influence our ability to identify shifts in diversification rate? For several large angiosperm clades (Angiospermae, Monocotyledonae, Orchidaceae, Poaceae, Eudicotyledonae, Fabaceae, and Asteraceae), we explore this issue by contrasting two approaches: (1) using small backbone trees with an inferred number of extant species assigned to each terminal clade and (2) using a mega-phylogeny of 55473 seed plant species represented in GenBank. The mega-phylogeny approach assumes that the...

Data from: Hybridization masks speciation in the evolutionary history of the Galápagos marine iguana

Amy MacLeod, Ariel Rodríguez, Miguel Vences, Pablo Orozco-TerWengel, Carolina García, Fritz Trillmich, Gabriele Gentile, Adalgisa Caccone, Galo Quezada & Sebastian Steinfartz
The effects of the direct interaction between hybridization and speciation—two major contrasting evolutionary processes—are poorly understood. We present here the evolutionary history of the Galápagos marine iguana (Amblyrhynchus cristatus) and reveal a case of incipient within-island speciation, which is paralleled by between-island hybridization. In-depth genome-wide analyses suggest that Amblyrhynchus diverged from its sister group, the Galápagos land iguanas, around 4.5 million years ago (Ma), but divergence among extant populations is exceedingly young (less than 50...

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