522 Works

Data from: Integrative testing of how environments from the past to the present shape genetic structure across landscapes

Qixin He, Danielle L. Edwards & L. Lacey Knowles
Tests of the genetic structure of empirical populations typically focus on the correlative relationships between population connectivity and geographic and/or environmental factors in landscape genetics. However, such tests may overlook or misidentify the impact of such factors on genetic structure, especially when connectivity patterns differ between past and present populations because of shifting environmental conditions over time. Here we account for the underlying demographic component of population connectivity associated with a temporarily dynamic landscape in...

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: 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: C4 photosynthesis boosts growth by altering physiology, allocation and size

Rebecca R. L. Atkinson, Emily J. Mockford, Christopher Bennett, Pascal-Antoine Christin, Elizabeth L. Spriggs, Robert P. Freckleton, Ken Thompson, Mark Rees & Colin P. Osborne
C4 photosynthesis is a complex set of leaf anatomical and biochemical adaptations that have evolved more than 60 times to boost carbon uptake compared with the ancestral C3 photosynthetic type1,​2,​3. Although C4 photosynthesis has the potential to drive faster growth rates4,5, experiments directly comparing C3 and C4 plants have not shown consistent effects1,6,7. This is problematic because differential growth is a crucial element of ecological theory8,9 explaining C4 savannah responses to global change10,11, and research...

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 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: Fear of predation slows plant-litter decomposition

Dror Hawlena, Michael S. Stickland, Mark A. Bradford & Oswald J. Schmitz
Aboveground consumers are believed to affect ecosystem functioning by regulating the quantity and quality of plant-litter entering the soil. We uncover a novel pathway whereby terrestrial predators regulate ecosystem processes via indirect control over soil community function. Grasshopper herbivores stressed by spider predators have a higher body carbon-to-nitrogen ratio than grasshoppers raised without spiders. This change in elemental content does not slow grasshopper decomposition but perturbs belowground community function, decelerating subsequent decomposition of plant-litter. This...

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: Deep phylogenomics of a tandem-repeat galectin regulating appendicular skeletal pattern formation

Ramray Bhat, Mahul Chakraborty, Tilmann Glimm, Thomas A. Stewart & Stuart A. Newman
Background: A multiscale network of two galectins Galectin-1 (Gal-1) and Galectin-8 (Gal-8) patterns the avian limb skeleton. Among vertebrates with paired appendages, chondrichthyan fins typically have one or more cartilage plates and many repeating parallel endoskeletal elements, actinopterygian fins have more varied patterns of nodules, bars and plates, while tetrapod limbs exhibit tandem arrays of few, proximodistally increasing numbers of elements. We applied a comparative genomic and protein evolution approach to understand the origin of...

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: Plant-soil feedbacks shift from negative to positive with decreasing light in forest understory species

Lauren M. Smith & Heather L. Reynolds
Net pairwise plant–soil feedbacks (PSF) may be an important factor structuring plant communities, yet the influence of abiotic context on PSF is not yet understood. Abiotic factors such as light availability can alter plant–soil interactions, potentially resulting in strong context dependence of PSF. Here, we present an experiment in which we measured whole-soil net pairwise feedbacks amongst six common forest understory species across a gradient of light availability. Light treatments were imposed throughout both phases...

Data from: State dependence, personality, and plants: light-foraging decisions in Mimosa pudica (L.)

Franz W. Simon, Christina N. Hodson & Bernard R. Roitberg
Plants make foraging decisions that are dependent on ecological conditions, such as resource availability and distribution. Despite the field of plant behavioral ecology gaining momentum, ecologists still know little about what factors impact plant behavior, especially light-foraging behavior. We made use of the behavioral reaction norm approach to investigate light foraging in a plant species that exhibits rapid movement: Mimosa pudica. We explored how herbivore avoidance behavior in M. pudica (which closes its leaflets temporarily...

Data from: Geographic population structure of the African malaria vector Anopheles gambiae suggests a role for the forest-savannah biome transition as a barrier to gene flow

Joao Pinto, Alexander Egyir-Yawson, José L. Vicente, Bruno Gomes, Federica Santalomazza, Marta Moreno, Jacques D. Charlwood, Frederic Simard, Nohal Elissa, David Weetman, Martin J. Donnelly, Adalgisa Caccone, Alessandra Della Torre, Caccone A, Simard F, Pinto J, Vicente JL, Gomes B, Elissa N, Weetman D & Donnelly MJ
The primary Afrotropical malaria mosquito vector Anopheles gambiae sensu stricto has a complex population structure. In western Africa, this species is split into two molecular forms and displays local and regional variation in chromosomal arrangements and behaviours. To investigate patterns of macro-geographic population substructure, 25 An. gambiae samples from 12 African countries were genotyped at 13 microsatellite loci. This analysis detected the presence of additional population structuring, with the M-form being subdivided into distinct west,...

Data from: Large fluctuations in the effective population size of the malaria mosquito Anopheles gambiae s.s. during vector control cycle

Theresa K. Hodges, Giridhar Athrey, Kevin C. Deitz, Hans J. Overgaard, Abrahan Matias, Aldalgisa Caccone, Michel A. Slotman & Adalgisa Caccone
On Bioko Island, Equatorial Guinea, indoor residual spraying (IRS) has been part of the Bioko Island Malaria Control Project since early 2004. Despite success in reducing childhood infections, areas of high transmission remained on the island. We therefore examined fluctuations in the effective population size (N_e) of the malaria vector Anopheles gambiae in an area of persistent high transmission over two spray rounds. We analyzed data for 13 microsatellite loci from 791 An. gambiae specimens...

Data from: Networks, trees, and treeshrews: assessing support and identifying conflict with multiple loci and a problematic root

Trina E. Roberts, Eric J. Sargis & Link E. Olson
Multiple unlinked genetic loci often provide a more comprehensive picture of evolutionary history than any single gene can, but analyzing multigene data presents particular challenges. Differing rates and patterns of nucleotide substitution, combined with the limited information available in any data set, can make it difficult to specify a model of evolution. In addition, conflict among loci can be the result of real differences in evolutionary process or of stochastic variance and errors in reconstruction....

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: 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: 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: 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: 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: Electrophoretic mobility confirms reassortment bias among geographic isolates of segmented RNA phages

Samuel L. Díaz-Muñoz, Olivier Tenaillon, Daniel Goldhill, Kristen Brao, Paul E. Turner & Lin Chao
Background: Sex presents evolutionary costs and benefits, leading to the expectation that the amount of genetic exchange should vary in conditions with contrasting cost-benefit equations. Like eukaryotes, viruses also engage in sex, but the rate of genetic exchange is often assumed to be a relatively invariant property of a particular virus. However, the rates of genetic exchange can vary within one type of virus according to geography, as highlighted by phylogeographic studies of cystoviruses. Here...

Data from: Climate change impacts on bumblebees converge across continents

Jeremy T. Kerr, Alana Pindar, Paul Galpern, Laurence Packer, Stuart M. Roberts, Pierre Rasmont, Oliver Schweiger, Sheila R. Colla, Leif L. Richardson, David L. Wagner, Lawrence F. Gall, Derek S. Sikes & Alberto Pantoja
For many species, geographical ranges are expanding toward the poles in response to climate change, while remaining stable along range edges nearest the equator. Using long-term observations across Europe and North America over 110 years, we tested for climate change–related range shifts in bumblebee species across the full extents of their latitudinal and thermal limits and movements along elevation gradients. We found cross-continentally consistent trends in failures to track warming through time at species’ northern...

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

Stephen A. Smith, Jeremy M. Beaulieu, Alexandros Stamatakis & Michael J. Donoghue
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...

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...

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...

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