130 Works

Variable prediction accuracy of polygenic scores within an ancestry group

Hakhamanesh Mostafavi, Arbel Harpak, Ipsita Agarwal, Dalton Conley, Jonathan Pritchard & Molly Przeworski
Fields as diverse as human genetics and sociology are increasingly using polygenic scores based on genome-wide association studies (GWAS) for phenotypic prediction. However, recent work has shown that polygenic scores have limited portability across groups of different genetic ancestries, restricting the contexts in which they can be used reliably and potentially creating serious inequities in future clinical applications. Using the UK Biobank data, we demonstrate that even within a single ancestry group (i.e., when there...

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...

Dust and Starlight Maps for Galaxies in the KINGFISH Sample

B.T. Draine, G. Aniano, L.K. Hunt, K. Sandstrom, D. Calzetti, R.C. Kennicutt, D.A. Dale, M. Galametz, K.D. Gordon, A.K. Leroy, J.-D.T. Smith, H. Roussel, M. Sauvage, F. Walter, L. Armus, A.D. Bolatto, M. Boquien, A. Crocker, I. De Looze, J. Donovan Meyer, G. Helou, J. Hinz, B.D. Johnson, J. Koda, A. Miller … & C.W. Engelbracht
Dust and starlight have been modeled for the KINGFISH project galaxies. For each pixel in each galaxy, we estimate: (1) dust surface density; (2) q_PAH, the dust mass fraction in PAHs; (3) distribution of starlight intensities heating the dust; (4) luminosity emitted by the dust; and (5) dust luminosity from regions with high starlight intensity.

Eco-evolutionary significance of 'loners'

Corina Tarnita, Fernando Rossine, Ricardo Martinez-Garcia, Allyson Sgro & Thomas Gregor
Loners, individuals out-of-sync with a coordinated majority, occur frequently in nature. Are loners incidental byproducts of large-scale coordination attempts or are they part of a mosaic of life-history strategies? Here, we provide empirical evidence of naturally occurring heritable variation in loner behavior in the model social amoeba Dictyostelium discoideum. We propose that Dictyostelium loners—cells that do not join the multicellular life-stage—arise from a dynamic population-partitioning process, the result of each cell making a stochastic, signal-based...

Nitrogen fixation and phosphatase activity of 97 nitrogen-fixing and non-fixing trees in Panama

S.A. Batterman, J.S. Hall, B. Turner, L.O. Hedin, J.K. LaHaela Walter, P. Sheldon & M. Van Breugel
This data includes information about nitrogen fixation, phosphatase activity, plant nitrogen and phosphorus demand and soil nitrogen and phosphorus availability of nitrogen-fixing and non-fixing trees from seven species grown in an experimental plantation at the Agua Salud Native Species Plantation, El Giral, Panama (9°12'50.15''N, 79°43'26''W). Data were collected by the Smithsonian Tropical Research Institute and Princeton University and were analysed by the University of Leeds. This work was funded by the following organisations: Heising-Simons Foundation,...

Data from: Quantifying water requirements of African ungulates through a combination of functional traits

Michiel Veldhuis, Emilian Kihwele, Victor Mchomvu, Norman Owen-Smith, Robyn Hetem, Matthew Hutchinson, Arjun Potter & Han Olff
Climate and land use change modify surface water availability in African savannas. Surface water is a key resource for both wildlife and livestock and its spatial and temporal distribution is important for understanding the composition of large herbivore assemblages in savannas. Yet, the extent to which ungulate species differ in their water requirements remains poorly quantified. Here, we infer the water requirements of 48 African ungulates by combining six different functional traits related to physiological...

Data from: The Achilles' heel hypothesis: misinformed keystone individuals impair collective learning and reduce group success

Jonathan Pruitt, Colin Wright, Carl Keiser, Alexander DeMarco, Matt Grobis, Noa Pinter-Wollman, Matthew M. Grobis, Alex E. DeMarco, Carl N. Keiser, Jonathan N. Pruitt & Colin M. Wright
Many animal societies rely on highly influential keystone individuals for proper functioning. When information quality is important for group success, such keystone individuals have the potential to diminish group performance if they possess inaccurate information. Here we test whether information quality (accurate or inaccurate) influences collective outcomes when keystone individuals are the first to acquire it. We trained keystone or generic individuals to attack or avoid novel stimuli and implanted these seed individuals within groups...

Data from: Whole-chromosome hitchhiking driven by a male-killing endosymbiont

Simon Martin, Kumar Singh, Ian Gordon, Kennedy Omufwoko, Steve Collins, Ian Warren, Hannah Munby, Oskar Brattström, Walther Traut, Dino Martins, David Smith, Chris Jiggins, Chris Bass & Richard French-Constant
Neo-sex chromosomes are found in many taxa, but the forces driving their emergence and spread are poorly understood. The female-specific neo-W chromosome of the African monarch (or queen) butterfly Danaus chrysippus presents an intriguing case study because it is restricted to a single ‘contact zone’ population, involves a putative colour patterning supergene, and co-occurs with infection by the the male-killing endosymbiont Spiroplasma. We investigated the origin and evolution of this system using whole genome sequencing....

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...

Vaccine driven virulence evolution: Consequences of unbalanced reductions in mortality and transmission and implications for pertussis vaccines

Ian Miller & C. Jessica Metcalf
Many vaccines have heterogenous effects across individuals. Additionally, some vaccines do not prevent infection, but reduce disease-associated mortality and transmission. Both of these factors will alter selection pressures on pathogens, and thus shape the evolution of pathogen virulence. We use a mathematical modeling framework to show that 1. the balance of how vaccines reduce transmission vs. mortality, and 2. individual variability in protection conferred, both shape the evolution of pathogen virulence. Epidemiological (burden of disease)...

An experimental test of community-based strategies for mitigating human-wildlife conflict around protected areas

Ryan Long, Paola Branco, Jerod Merkle, Robert Pringle, Lucy King, Tosca Tindall & Marc Stalmans
Natural habitats are rapidly being converted to cultivated croplands, and crop-raiding by wildlife threatens both wildlife conservation and human livelihoods worldwide. We combined movement data from GPS-collared elephants with camera-trap data and local reporting systems in a before-after-control-impact design to evaluate community-based strategies for reducing crop raiding outside Mozambique’s Gorongosa National Park. All types of experimental fences tested (beehive, chili, beehive and chili combined, and procedural controls) significantly reduced the number of times elephants left...

Data from: Phenological plasticity is a poor predictor of subalpine plant population performance following experimental climate change

Sebastian Block, Jake Alexander & Jonathan Levine
Phenological shifts, changes in the seasonal timing of life cycle events, are among the best documented responses of species to climate change. However, the consequences of these phenological shifts for population dynamics remain unclear. Population growth could be enhanced if species that advance their phenology benefit from longer growing seasons and gain a pre-emptive advantage in resource competition. However, it might also be reduced if phenological advances increase exposure to stresses, such as herbivores and,...

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: Vocal state change through laryngeal development

Yisi S. Zhang, Daniel Y. Takahashi, Diana A. Liao, Asif A. Ghazanfar & Coen P. H. Elemans
Across vertebrates, progressive changes in vocal behavior during postnatal development are typically attributed solely to developing neural circuits. How the changing body influences vocal development remains unknown. Here we show that state changes in the contact vocalizations of infant marmoset monkeys, which transition from noisy, low frequency cries to tonal, higher pitched vocalizations in adults, are caused partially by laryngeal development. Combining analyses of natural vocalizations, motorized excised larynx experiments, tensile material tests and high-speed...

Data from: Covariation of diet and gut microbiome in African megafauna

Tyler R. Kartzinel, Julianna C. Hsing, Paul M. Musili, Bianca R. P. Brown & Robert M. Pringle
A major challenge in biology is to understand how phylogeny, diet, and environment shape the mammalian gut microbiome. Yet most studies of non-human microbiomes have relied on relatively coarse dietary categorizations and have focused either on individual wild populations or on captive animals that are sheltered from environmental pressures, which may obscure the effects of dietary and environmental variation on microbiome composition in diverse natural communities. We analyzed plant and bacterial DNA in fecal samples...

Data from: Forest-type specialization strongly predicts avian responses to tropical agriculture

Jacob B. Socolar & David S. Wilcove
Species’ traits influence how populations respond to land-use change. However, even in well-characterized groups such as birds, widely studied traits explain only a modest proportion of the variance in response across species. Here, we show that associations with particular forest types strongly predict the sensitivity of forest-dwelling Amazonian birds to agriculture. Incorporating these fine-scale habitat associations into models of population response dramatically improves predictive performance and markedly outperforms the functional traits that commonly appear in...

Data from: Measuring fecal testosterone in females and fecal estrogens in males: comparison of RIA and LC/MS/MS methods for wild baboons (Papio cynocephalus).

Laurence R. Gesquiere, Toni E. Ziegler, Patricia A. Chen, Katherine A. Epstein, Susan C. Alberts & Jeanne Altmann
The development of non-invasive methods, particularly fecal determination, has made possible the assessment of hormone concentrations in wild animal populations. However, measuring fecal metabolites needs careful validation for each species and for each sex. We investigated whether radioimmunoassays (RIAs) previously used to measure fecal testosterone (fT) in male baboons and fecal estrogens (fE) in female baboons were well suited to measure these hormones in the opposite sex. We compared fE and fT concentrations determined by...

Data from: Social networks predict gut microbiome composition in wild baboons

Jenny Tung, Luis B. Barriero, Michael B. Burns, J. C. Grenier, Josh Lynch, L. E. Grieneisen, J. Altmann, S. C. Alberts, R. Blekhman, E. A. Archie, Laura E Grieneisen, Elizabeth A Archie, Susan C Alberts, Jeanne Altmann, Luis B Barreiro, Jean-Christophe Grenier, Michael B Burns & Ran Blekhman
Social relationships have profound effects on health in humans and other primates, but the mechanisms that explain this relationship are not well understood. Using shotgun metagenomic data from wild baboons, we found that social group membership and social network relationships predicted both the taxonomic structure of the gut microbiome and the structure of genes encoded by gut microbial species. Rates of interaction directly explained variation in the gut microbiome, even after controlling for diet, kinship,...

Data from: Reliable, verifiable and efficient monitoring of biodiversity via metabarcoding

Yinqiu Ji, Louise Ashton, Scott M. Pedley, David P. Edwards, Yong Tang, Akihiro Nakamura, Roger Kitching, Paul M. Dolman, Paul Woodcock, Felicity A. Edwards, Trond H. Larsen, Wayne W. Hsu, Suzan Benedick, Keith C. Hamer, David S. Wilcove, Catharine Bruce, Xiaoyang Wang, Taal Levi, Martin Lott, Brent C. Emerson & Douglas W. Yu
To manage and conserve biodiversity, one must know what is being lost, where, and why, as well as which remedies are likely to be most effective. Metabarcoding technology can characterise the species compositions of mass samples of eukaryotes or of environmental DNA. Here, we validate metabarcoding by testing it against three high-quality standard data sets that were collected in Malaysia (tropical), China (subtropical) and the United Kingdom (temperate) and that comprised 55,813 arthropod and bird...

Data from: High-molecular-weight polymers from dietary fiber drive aggregation of particulates in the murine small intestine

Asher Preska Steinberg, Sujit S. Datta, Thomas Naragon, Justin C. Rolando, Said R. Bogatyrev, Rustem F. Ismagilov, Sujit S Datta, Said R Bogatyrev, Rustem F Ismagilov & Justin C Rolando
The lumen of the small intestine (SI) is filled with particulates: microbes, therapeutic particles, and food granules. The structure of this particulate suspension could impact uptake of drugs and nutrients and the function of microorganisms; however, little is understood about how this suspension is re-structured as it transits the gut. Here, we demonstrate that particles spontaneously aggregate in SI luminal fluid ex vivo. We find that mucins and immunoglobulins are not required for aggregation. Instead,...

Data from: Evolution of eye morphology and rhodopsin expression in the Drosophila melanogaster species subgroup

Nico Posnien, Corinna Hopfen, Maarten Hilbrant, Margarita Ramos-Womack, Sophie Murat, Anna Schönauer, Samantha L. Herbert, Maria D. S. Nunes, Saad Arif, Casper J. Breuker, Christian Schlötterer, Philipp Mitteroeker, Alistair P. McGregor & Philipp Mitteroecker
A striking diversity of compound eye size and shape has evolved among insects. The number of ommatidia and their size are major determinants of the visual sensitivity and acuity of the compound eye. Each ommatidium is composed of eight photoreceptor cells that facilitate the discrimination of different colours via the expression of various light sensitive Rhodopsin proteins. It follows that variation in eye size, shape, and opsin composition is likely to directly influence vision. We...

Data from: Self-organizing dominance hierarchies in a wild primate population

Mathias Franz, Emily McLean, Jenny Tung, Jeanne Altmann & Susan C. Alberts
Linear dominance hierarchies, which are common in social animals, can profoundly influence access to limited resources, reproductive opportunities and health. In spite of their importance, the mechanisms that govern the dynamics of such hierarchies remain unclear. Two hypotheses explain how linear hierarchies might emerge and change over time. The ‘prior attributes hypothesis’ posits that individual differences in fighting ability directly determine dominance ranks. By contrast, the ‘social dynamics hypothesis’ posits that dominance ranks emerge from...

Data from: Irrational time allocation in decision-making

Bastiaan Oud, Ian M. Krajbich, Kevin Miller, Jin Cheong, Matthew Botvinick, Ernst Fehr, Jin Hyun Cheong & Ian Krajbich
Time is an extremely valuable resource but little is known about the efficiency of time allocation in decision making. Empirical evidence suggests that in many ecologically relevant situations, decision difficulty and the relative reward from making a correct choice, compared to an incorrect one, are inversely linked, implying that it is optimal to use relatively less time for difficult choice problems. This applies, in particular, to value-based choices, in which the relative reward from choosing...

Data from: On the evolutionary interplay between dispersal and local adaptation in heterogeneous environments

Andrew M. Berdahl, Colin J. Torney, Emmanuel Schertzer, Simon A. Levin & Andrew Berdahl
Dispersal, whether in the form of a dandelion seed drifting on the breeze, or a salmon migrating upstream to breed in a non-natal stream, transports genes between locations. At these locations, local adaptation modifies the gene frequencies so their carriers are better suited to particular conditions, be those of newly disturbed soil or a quiet river pool. Both dispersal and local adaptation are major drivers of population structure; however, in general, their respective roles are...

Data from: A single-nucleotide polymorphism-based approach for rapid and cost-effective genetic wolf monitoring in Europe based on noninvasively collected samples

Robert H. S. Kraus, Bridgett VonHoldt, Berardino Cocchiararo, Verena Harms, Helmut Bayerl, Ralph Kühn, Daniel W. Förster, Jörns Fickel, Christian Roos & Carsten Nowak
Noninvasive genetics based on microsatellite markers has become an indispensable tool for wildlife monitoring and conservation research over the past decades. However, microsatellites have several drawbacks, such as the lack of standardisation between laboratories and high error rates. Here, we propose an alternative single-nucleotide polymorphism (SNP)-based marker system for noninvasively collected samples, which promises to solve these problems. Using nanofluidic SNP genotyping technology (Fluidigm), we genotyped 158 wolf samples (tissue, scats, hairs, urine) for 192...

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