333 Works

Data from: The ecology of a continental evolutionary radiation: Is the radiation of sigmodontine rodents adaptive?

Renan Maestri, Leandro Rabello Monteiro, Rodrigo Fornel, Nathan S. Upham, Bruce D. Patterson, Thales Renato O. De Freitas & Thales Renato Ochotorena De Freitas
Evolutionary radiations on continents are less well-understood and appreciated than those occurring on islands. The extent of ecological influence on species divergence can be evaluated to determine whether a radiation was ultimately the outcome of divergent natural selection or else arose mainly by nonecological divergence. Here, we used phylogenetic comparative methods to test distinct hypotheses corresponding to adaptive and nonadaptive evolutionary scenarios for the morphological evolution of sigmodontine rodents. Results showed that ecological variables (diet...

Data from: Inferring pathobiology from structural MRI in schizophrenia and bipolar disorder: modeling head motion and neuroanatomical specificity

Nailin Yao, Anderson M. Winkler, Jennifer Barrett, Gregory A. Book, Tamara Beetham, Rachel Horseman, Olivia Leach, Karen Hodgson, Emma E. Knowles, Samuel Mathias, Michael C. Stevens, Michal Assaf, Theo G. M. Van Erp, Godfrey D. Pearlson & David C. Glahn
Despite over 400 peer-reviewed structural MRI publications documenting neuroanatomic abnormalities in bipolar disorder and schizophrenia, the confounding effects of head motion and the regional specificity of these defects are unclear. Using a large cohort of individuals scanned on the same research dedicated MRI with broadly similar protocols, we observe reduced cortical thickness indices in both illnesses, though less pronounced in bipolar disorder. While schizophrenia (n = 226) was associated with wide-spread surface area reductions, bipolar...

Data from: Gradual loading ameliorates maladaptation in computational simulations of vein graft growth and remodelling

Abhay Bangalore Ramachandra, Jay D. Humphrey & Alison L. Marsden
Vein graft failure is a prevalent problem in vascular surgeries, including bypass grafting and arteriovenous fistula procedures in which veins are subjected to severe changes in pressure and flow. Animal and clinical studies provide significant insight, but understanding the complex underlying coupled mechanisms can be advanced using computational models. Towards this end, we propose a new model of venous growth and remodelling (G&R) based on a constrained mixture theory. First, we identify constitutive relations and...

Data from: Group augmentation, collective action, and territorial boundary patrols by male chimpanzees

Kevin E. Langergraber, David P. Watts, Linda Vigilant & John C. Mitani
How can collective action evolve when individuals benefit from cooperation regardless of whether they pay its participation costs? According to one influential perspective, collective action problems are common, especially when groups are large, but may be solved when individuals who have more to gain from the collective good or can produce it at low costs provide it to others as a byproduct. Several results from a 20-y study of one of the most striking examples...

Data from: Linking functional diversity and ecosystem processes: a framework for using functional diversity metrics to predict the ecosystem impact of functionally unique species

Sara E. Kuebbing, Daniel S. Maynard & Mark A. Bradford
1.Functional diversity (FD) metrics are widely used to assess invasion ecosystem impacts, but we have limited theory to predict how FD should respond to invasion. A key challenge to effectively using FD metrics is the complexity of conceptualizing alterations to multi-dimensional trait space, making it difficult to select a priori the most appropriate metric for specific ecological questions. 2.Here, we provide expectations on how invasion should change four commonly used FD metrics—functional richness (FRic), evenness...

Data from: Different clades and traits yield similar grassland functional responses

Elisabeth J. Forrestel, Michael J. Donoghue, Erika J. Edwards, Walter Jetz, Justin C. O. Du Toit & Melinda D. Smith
Plant functional traits are viewed as key to predicting important ecosystem and community properties across resource gradients within and among biogeographic regions. Vegetation dynamics and ecosystem processes, such as aboveground net primary productivity (ANPP), are increasingly being modeled as a function of the quantitative traits of species, which are used as proxies for photosynthetic rates, and nutrient and water-use efficiency. These approaches rely on an assumption that a certain trait value consistently confers a specific...

Data from: Interpreting and predicting the spread of invasive wild pigs

Nathan P. Snow, Marta A. Jarzyna & Kurt C. VerCauteren
The eruption of invasive wild pigs (IWPs) Sus scrofa throughout the world exemplifies the need to understand the influences of exotic and non-native species expansions. In particular, the continental USA is precariously threatened by a rapid expansion of IWPs, and a better understanding of the rate and process of spread can inform strategies that will limit the expansion. We developed a spatially and temporally dynamic model to examine three decades (1982–2012) of IWP expansion, and...

Data from: The influence of a semi-arid sub-catchment on suspended sediments in the Mara River, Kenya

Christopher L. Dutton, Amanda L. Subalusky, Shimon C. Anisfeld, Laban Njoroge, Emma J. Rosi & David M. Post
The Mara River Basin in East Africa is a trans-boundary basin of international significance experiencing excessive levels of sediment loads. Sediment levels in this river are extremely high (turbidities as high as 6,000 NTU) and appear to be increasing over time. Large wildlife populations, unregulated livestock grazing, and agricultural land conversion are all potential factors increasing sediment loads in the semi-arid portion of the basin. The basin is well-known for its annual wildebeest (Connochaetes taurinus)...

Data from: An inverse latitudinal gradient in speciation rate for marine fishes

Daniel L. Rabosky, Jonathan Chang, Pascal O. Title, Peter F. Cowman, Lauren Sallan, Matt Friedman, Kristin Kaschner, Cristina Garilao, Thomas J. Near, Marta Coll & Michael E. Alfaro
Far more species of organisms are found in the tropics than in temperate and polar regions, but the evolutionary and ecological causes of this pattern remain controversial1,2. Tropical marine fish communities are much more diverse than cold-water fish communities found at higher latitudes3,4, and several explanations for this latitudinal diversity gradient propose that warm reef environments serve as evolutionary ‘hotspots’ for species formation5,6,7,8. Here we test the relationship between latitude, species richness and speciation rate...

Data from: Global geographic patterns in the colours and sizes of animal‐dispersed fruits

Miranda A. Sinnott-Armstrong, Alexander E. Downie, Sarah Federman, Alfredo Valido, Pedro Jordano & Michael J. Donoghue
Aim. Fruit colours attract animal seed dispersers, yet the causes of fruit colour diversity remain controversial. The lack of knowledge of large-scale spatial patterns in fruit colours has limited our ability to formulate and test alternative hypotheses to explain fruit colour, fruit size, and fruit colour diversity. We describe spatial (especially latitudinal) variation in fruit colour, colour diversity, and length, and test for correlations between fruit colour, length, and plant habit. Location. Global. Time period....

Data from: Population genomics through time provides insights into the consequences of decline and rapid demographic recovery through head-starting in a Galapagos giant tortoise

Evelyn L. Jensen, Danielle L. Edwards, Ryan C. Garrick, Joshua M. Miller, James P. Gibbs, Linda J. Cayot, Washington Tapia, Aldalgisa Caccone, Michael A. Russello & Adalgisa Caccone
Population genetic theory related to the consequences of rapid population decline is well-developed, but there are very few empirical studies where sampling was conducted before and after a known bottleneck event. Such knowledge is of particular importance for species restoration, given links between genetic diversity and the probability of long-term persistence. To directly evaluate the relationship between current genetic diversity and past demographic events, we collected genome-wide single nucleotide polymorphism data from pre-bottleneck historical (c.1906)...

Data from: Retracing the Hawaiian silversword radiation despite phylogenetic, biogeographic, and paleogeographic uncertainty

Michael J. Landis, William A. Freyman & Bruce G. Baldwin
The Hawaiian silversword alliance (Asteraceae) is an iconic adaptive radiation. However, like many island plant lineages, no fossils have been assigned to the clade. As a result, the clade's age and diversification rate are not known precisely, making it difficult to test biogeographic hypotheses about the radiation. Without fossils, paleogeographically structured biogeographic processes may inform species divergence times; for example, an island must first exist for a clade to radiate upon it. We date the...

Data from: Genetic effects of anthropogenic habitat fragmentation on remnant animal and plant populations: a meta-analysis

Daniel R. Schlaepfer, Brigitte Braschler, Hans-Peter Rusterholz & Bruno Baur
Habitat loss and fragmentation are among the biggest threats to biodiversity. Anthropogenic habitat fragmentation leads to small and isolated remnant plant and animal populations. The combination of increased random genetic drift, inbreeding, and reduced gene flow may substantially reduce genetic variation of remnant populations. However, the magnitude of these responses may depend on several poorly understood factors including organism group, habitat type of both the fragment and the surrounding matrix, life‐history traits, and time since...

Data from: Tracing the diversification history of a Neogene rodent invasion into South America

Renan Maestri, Nathan S. Upham & Bruce D. Patterson
We investigated spatial patterns of evolutionary relatedness and diversification rates to test hypotheses about the historical biogeographic processes underlying the radiation of Neotropical rats and mice (Sigmodontinae, ~400 species). A negative correlation between mean phylogenetic distance and diversification rates of rodent assemblages reveals a pattern of species co-occurrence in which assemblages of closely related species are also the fastest diversifying ones. Subregions of the Neotropics occupied by distantly related species that are on average more...

Data from: Optogenetically induced low-frequency correlations impair perception

Anirvan S. Nandy, Jonathan J. Nassi, Monika P. Jadi & John H. Reynolds
Deployment of covert attention to a spatial location can cause large decreases in low-frequency correlated variability among neurons in macaque area V4 whose receptive-fields lie at the attended location. It has been estimated that this reduction accounts for a substantial fraction of the attention-mediated improvement in sensory processing. These estimates depend on assumptions about how population signals are decoded and the conclusion that correlated variability impairs perception, is purely hypothetical. Here we test this proposal...

Data from: The diversity of population responses to environmental change

Fernando Colchero, Owen R. Jones, Dalia A. Conde, Dave Hodgson, Felix Zajitschek, Benedikt R. Schmidt, Aurelio F. Malo, Susan C. Alberts, Peter H. Becker, Sandra Bouwhuis, Anne M. Bronikowski, Kristel M. De Vleeschouwer, Richard J. Delahay, Stefan Dummermuth, Eduardo Fernández-Duque, John Frisenvænge, Martin Hesselsøe, Sam Larson, Jean-Francois Lemaitre, Jennifer McDonald, David A.W. Miller, Colin O'Donnell, Craig Packer, Becky E. Raboy, Christopher J. Reading … & Chris J. Reading
The current extinction and climate change crises pressure us to predict population dynamics with ever-greater accuracy. Although predictions rest on the well-advanced theory of age-structured populations, two key issues remain poorly-explored. Specifically, how the age-dependency in demographic rates and the year-to-year interactions between survival and fecundity affect stochastic population growth rates. We use inference, simulations, and mathematical derivations to explore how environmental perturbations determine population growth rates for populations with different age-specific demographic rates and...

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: The function of the ophiuroid nerve ring: how a decentralized nervous system controls coordinated locomotion

Elizabeth G. Clark, Daichi Kanauchi, Takeshi Kano, Hitoshi Aonuma, Derek E. G. Briggs & Akio Ishiguro
Echinoderms lack a centralized nervous control system yet each extant echinoderm class has evolved unique and effective strategies for locomotion. Brittle stars (Ophiuroidea) stride swiftly over the seafloor by coordinating motions of their five muscular arms. Their arms consist of many repeating segments, requiring them to use a complex control system to coordinate motions among segments and between arms. We conducted in vivo experiments with brittle stars to analyze the functional role of the nerve...

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...

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...

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...

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...

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...

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....

Data from: A phylogenomic resolution of the sea urchin tree of life

Nicolás Mongiardino Koch, Simon E. Coppard, Harilaos A. Lessios, Derek E.G. Briggs, Rich Mooi & Greg W. Rouse
Background: Echinoidea is a clade of marine animals including sea urchins, heart urchins, sand dollars and sea biscuits. Found in benthic habitats across all latitudes, echinoids are key components of marine communities such as coral reefs and kelp forests. A little over 1,000 species inhabit the oceans today, a diversity that traces its roots back at least to the Permian. Although much effort has been devoted to elucidating the echinoid tree of life using a...

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