635 Works

Data from: Genetic diversity and gene flow decline with elevation in montane mayflies

Nicholas R. Polato, Miranda M. Gray, Brian A. Gill, C. Guilherme Becker, K.L. Casner, Alex S. Flecker, Boris C. Kondratief, Andrea C. Encalada, N. LeRoy Poff, W. Chris Funk & Kelly R. Zamudio
Montane environments around the globe are biodiversity ‘hotspots’ and important reservoirs of genetic diversity. Montane species are also typically more vulnerable to environmental change than their low-elevation counterparts due to restricted ranges and dispersal limitations. Here we focus on two abundant congeneric mayflies (Baetis bicaudatus and B. tricaudatus) from montane streams over an elevation gradient spanning 1400 m. Using single-nucleotide polymorphism genotypes, we measured population diversity and vulnerability in these two species by: (i) describing...

Data from: Campylobacter jejuni infection associated with relatively poor condition and low survival in a wild bird

Conor C. Taff & Andrea K. Townsend
Campylobacter jejuni is the most common foodborne pathogen in industrialized countries. Most human infections come from contaminated poultry, but wild birds are also known to harbor C. jejuni. Wild birds are often described as asymptomatic carriers, but this assumption is based on domestic poultry research. We studied the effects of C. jejuni infection on body condition and survival of adult and nestling American crows Corvus brachyrhynchos in Davis, California. Previous work demonstrated that more than...

Data from: The fate of phosphorus fertilizer in Amazon soya bean fields

Shelby H. Riskin, Stephen Porder, Christopher Neill, Adelaine Michela E Silva Figueira, Carmen Tubbesing & Natalie Mahowald
Fertilizer-intensive soya bean agriculture has recently expanded in southeastern Amazônia, and whereas intensive fertilizer use in the temperate zone has led to widespread eutrophication of freshwater ecosystems, the effects in tropical systems are less well understood. We examined the fate of fertilizer P by comparing P forms and budgets across a chronosequence of soya bean fields (converted to soya beans between 2003 and 2008) and forests on an 800 km2 soya bean farm in Mato...

Data from: Range-wide genomic data synthesis reveals transatlantic vicariance and secondary contact in Atlantic cod

Robert Fairweather, Ian R. Bradbury, Sarah J. Heylar, Mark De Bruyn, Nina O. Therkildsen, Paul Bentzen, Jakob Hemmer-Hansen & Gary R. Carvalho
Recent advances in genetic and genomic analysis have greatly improved our understanding of spatial population structure in marine species. However, studies addressing phylogeographic patterns at oceanic spatial scales remain rare. In Atlantic cod (Gadus morhua), existing range‐wide examinations suggest significant transatlantic divergence, although the fine‐scale contemporary distribution of populations and potential for secondary contact are largely unresolved. Here, we explore transatlantic phylogeography in Atlantic cod using a data‐synthesis approach, integrating multiple genome‐wide single‐nucleotide polymorphism (SNP)...

Data from: Domesticated honeybees facilitate interspecific hybridization between two Taraxacum congeners

Youhong Peng, Yuran Dong, Haigen Xu, Xinqiang Xi, Karl J. Niklas & Shucun Sun
1. Interspecific hybridization is common in plants under natural conditions, but the ecological mechanisms underlying when and how it happens have not fully been understood. 2. Taraxacum calanthodium and T. lugubre are two herbaceous annals co-occurring in alpine meadows of the eastern Tibetan Plateau that share the same pollinators including domestic honeybees during their overlapping flowering times. Because honeybees tend to visit flowers less discriminatively when bee densities are high, we hypothesized that intense apiculture...

Data from: The importance of terrestrial subsidies in stream food webs varies along a stream size gradient

Sarah M. Collins, Tyler J. Kohler, Steven A. Thomas, William W. Fetzer & Alexander S. Flecker
Cross system subsidies of energy and materials can be a substantial fraction of food web fluxes in ecosystems, especially when autochthonous production is strongly limited by light or nutrients. We explored whether assimilation of terrestrial energy varied in specific consumer taxa collected from streams of different sizes and resource availabilities. Since headwater streams are often unproductive, we expected that inputs from surrounding terrestrial systems (i.e. leaf litter, terrestrial invertebrates) would be a more important food...

Data from: Long-term avian community response to housing development at the boundary of U.S. protected areas: effect size increases with time

Eric M. Wood, Anna M. Pidgeon, Volker C. Radeloff, David P. Helmers, Patrick D. Culbert, Nicholas S. Keuler & Curtis H. Flather
1. Biodiversity conservation is a primary function of protected areas. However, protected areas also attract people, and therefore, land use has intensified at the boundaries of these lands globally. In the USA, since the 1970s, housing growth at the boundaries (<1 km) of protected areas has increased at a rate far higher than on more distant private lands. Here, we designed our analyses to address our central hypothesis that increasing housing density in and near...

Data from: Modeling strategic sperm allocation: tailoring the predictions to the species

Biz R. Turnell, Kerry L. Shaw & Hudson Kern Reeve
Two major challenges exist when empirically testing the predictions of sperm allocation theory. First, the study species must adhere to the assumptions of the model being tested. Unfortunately, the common assumption of sperm allocation models that females mate a maximum of once or twice does not hold for many, if not most, multiply and sequentially mating animals. Second, a model’s parameters, which dictate its predictions, must be measured in the study species. Common examples of...

Data from: On the origin of a domesticated species: identifying the parent population of Russian silver foxes (Vulpes vulpes)

Mark J. Statham, Lyudmila N. Trut, Ben N. Sacks, Anastasiya V. Kharlamova, Irina N. Oskina, Rimma G. Gulevich, Jennifer L. Johnson, Svetlana V. Temnykh, Gregory M. Acland & Anna V. Kukekova
The foxes at Novosibirsk, Russia, are the only population of domesticated foxes in the world. These domesticated foxes originated from farm-bred silver foxes (Vulpes vulpes), whose genetic source is unknown. In the present study, we examined the origin of the domesticated strain of foxes and two other farm-bred fox populations (aggressive and unselected) maintained in Novosibirsk. To identify the phylogenetic origin of these populations we sequenced two regions of mitochondrial DNA, cytochrome b and d-loop,...

Data from: Seagrass ecosystems reduce exposure to bacterial pathogens of humans, fishes and invertebrates

Joleah B. Lamb, Jeroen A. J. M. Van De Water, David G. Bourne, Craig Altier, Margaux Y. Hein, Evan A. Fiorenza, Nur Abu, Jamaluddin Jompa & C. Drew Harvell
Plants are important in urban environments for removing pathogens and improving water quality. Seagrass meadows are the most widespread coastal ecosystem on the planet. Although these plants are known to be associated with natural biocide production, they have not been evaluated for their ability to remove microbiological contamination. Using amplicon sequencing of the 16S ribosomal RNA gene, we found that when seagrass meadows are present, there was a 50% reduction in the relative abundance of...

Data from: A new subfamily classification of the Leguminosae based on a taxonomically comprehensive phylogeny

, Anne Bruneau, Nasim Azani, Marielle Babineau, Edeline Gagnon, Carole Sinou, Royce Steeves, Erin Zimmerman, C. Donovan Bailey, Lynsey Kovar, Madhugiri Nageswara-Rao, Hannah Banks, RuthP. Clark, Manuel De La Estrella, Peter Gasson, GeoffreyC. Kite, BenteB. Klitgaard, GwilymP. Lewis, Danilo Neves, Gerhard Prenner, María De Lourdes Rico-Arce, ArianeR. Barbosa, Maria Cristina López-Roberts, Luciano Paganucci De Queiroz, PétalaG. Ribeiro … & Tingshuang Yi
The classification of the legume family proposed here addresses the long-known non-monophyly of the traditionally recognised subfamily Caesalpinioideae, by recognising six robustly supported monophyletic subfamilies. This new classification uses as its framework the most comprehensive phylogenetic analyses of legumes to date, based on plastid matK gene sequences, and including near-complete sampling of genera (698 of the currently recognised 765 genera) and ca. 20% (3696) of known species. The matK gene region has been the most...

Data from: A voyage to Terra Australis: human-mediated dispersal of cats

Katrin Koch, Dave Algar, Jeremy B. Searle, Markus Pfenninger & Klaus Schwenk
Background. Cats have been transported as human commensals worldwide giving rise to many feral populations. In Australia, feral cats have caused decline and extinction of native mammals, but their time of introduction and origin is unclear. Here, we investigate hypotheses of cat arrival pre- or post-European settlement, and the potential for admixture between cats of different invasion events. We analyse the genetic structure and diversity of feral cats from six locations on mainland Australia, seven...

Data from: Differentially expressed genes match bill morphology and plumage despite largely homogenous genomes in a Holarctic songbird

Nicholas A. Mason & Scott A. Taylor
Understanding the patterns and processes that contribute to phenotypic diversity and speciation is a central goal of evolutionary biology. Recently, high-throughput sequencing has provided unprecedented phylogenetic resolution in many lineages that have experienced rapid diversification. The Holarctic redpoll finches (Genus: Acanthis) provide an intriguing example of a recent, phenotypically diverse lineage; traditional sequencing and genotyping methods have failed to detect any genetic differences between currently recognized species, despite marked variation in plumage and morphology within...

Data from: Gradual evolution towards flightlessness in Steamer-Ducks

Leonardo Campagna, Kevin G McCracken & Irby J. Lovette
Flightlessness in birds is the product of changes in suites of characters--including increased body size and reduced anterior limbs--that have evolved repeatedly and independently under similar ecological conditions (generally insularity). It remains unknown whether this phenotypic convergence extends to the genomic level, partially because many losses of flight occurred long ago (such as in penguins or ratites), thus complicating the study of the genetic pathways to flightlessness. Here we use genome sequencing to study the...

Data from: A phylogenetic backbone for Bivalvia: an RNA-seq approach

Vanessa L. González, Sónia C. S. Andrade, Rüdiger Bieler, Timothy M. Collins, Casey W. Dunn, Paula M. Mikkelsen, John D. Taylor, Gonzalo Giribet & V. L. Gonzalez
Bivalves are an ancient and ubiquitous group of aquatic invertebrates with an estimated 10 000–20 000 living species. They are economically significant as a human food source, and ecologically important given their biomass and effects on communities. Their phylogenetic relationships have been studied for decades, and their unparalleled fossil record extends from the Cambrian to the Recent. Nevertheless, a robustly supported phylogeny of the deepest nodes, needed to fully exploit the bivalves as a model...

Data from: Ancient host shifts followed by host conservatism in a group of ant parasitoids

Elizabeth A. Murray, Andrew E. Carmichael & John M. Heraty
While ant colonies serve as host to a diverse array of myrmecophiles, few parasitoids are able to exploit this vast resource. A notable exception is the wasp family Eucharitidae, which is the only family of insects known to exclusively parasitize ants. Worldwide, approximately 700 Eucharitidae species attack five subfamilies across the ant phylogeny. Our goal is to uncover the pattern of eucharitid diversification, including timing of key evolutionary events, biogeographic patterns and potential cophylogeny with...

Data from: When one phenotype is not enough - divergent evolutionary trajectories govern venom variation in a widespread rattlesnake species

Giulia Zancolli, Juan J. Calvete, Michael D. Cardwell, Harry W. Greene, William K. Hayes, Matthew J. Hegarty, Hans-Werner Herrmann, Andrew T. Holycross, Dominic I. Lannutti, John F. Mulley, Libia Sanz, Zachary D. Travis, Joshua R. Whorley, Catharine E. Wüster & Wolfgang Wuster
Understanding the origin and maintenance of phenotypic variation, particularly across a continuous spatial distribution, represents a key challenge in evolutionary biology. For this, animal venoms represent ideal study systems: they are complex, variable, yet easily quantifiable molecular phenotypes with a clear function. Rattlesnakes display tremendous variation in their venom composition, mostly through strongly dichotomous venom strategies, which may even coexist within single species. Here, through dense, widespread population-level sampling of the Mojave rattlesnake, Crotalus scutulatus,...

Data from: Identifying and reducing AFLP genotyping error: an example of tradeoffs when comparing population structure in broadcast spawning versus brooding oysters

Haibin Zhang & Matthew P. Hare
Phylogeographic inferences about gene flow are strengthened through comparison of co-distributed taxa, but also depend on adequate genomic sampling. Amplified Fragment Length Polymorphisms (AFLP) provide a rapid and inexpensive source of multilocus allele frequency data for making genomically robust inferences. Every AFLP study initially generates markers with a range of locus-specific genotyping error rates and applies criteria to select a subset for analysis. However, there has been very little empirical evaluation of the best tradeoff...

Data from: The genetic architecture of defence as resistance to and tolerance of bacterial infection in Drosophila melanogaster

Virginia M. Howick & Brian P. Lazzaro
Defence against pathogenic infection can take two forms: resistance and tolerance. Resistance is the ability of the host to limit a pathogen burden, whereas tolerance is the ability to limit the negative consequences of infection at a given level of infection intensity. Evolutionarily, a tolerance strategy that is independent of resistance could allow the host to avoid mounting a costly immune response and, theoretically, to avoid a co-evolutionary arms race between pathogen virulence and host...

Data from: Dissecting genome-wide association signals for loss-of-function phenotypes in sorghum flavonoid pigmentation traits

Geoffrey P. Morris, Davina H. Rhodes, Zachary Brenton, Punna Ramu, Vinayan Madhumal Thayil, Santosh Deshpande, C. Thomas Hash, Charlotte Acharya, Sharon E. Mitchell, Edward S. Buckler, Jianming Yu & Stephen Kresovich
Genome-wide association studies (GWAS) are a powerful method to dissect the genetic basis of traits, though in practice the effects of complex genetic architecture and population structure remain poorly understood. To compare mapping strategies we dissect the genetic control of flavonoid pigmentation traits in the cereal grass sorghum using high-resolution genotyping-by-sequencing (GBS) SNP markers. Studying the grain tannin trait, we find that General Linear Models (GLM) are not able to precisely map tan1-a, a known...

Data from: New insights into New World biogeography: an integrated view from the phylogeny of blackbirds, cardinals, sparrows, tanagers, warblers, and allies

F. Keith Barker, Kevin J. Burns, John Klicka, Scott M. Lanyon & Irby J. Lovette
Understanding the biogeographic origins and temporal sequencing of groups within a region or of lineages within an ecosystem can yield important insights into evolutionary dynamics and ecological processes. Fifty years ago, Ernst Mayr generated comprehensive—if limited—inferences about the origins of the New World avifaunas, including the importance of pre-Isthmian dispersal between North and South America. Since then, methodological advances have improved our ability to address many of the same questions, but the phylogenies upon which...

Data from: Agonistic character displacement in social cognition of advertisement signals

Bret Pasch, Rachel Sanford & Steven M. Phelps
Interspecific aggression between sibling species may enhance discrimination of competitors when recognition errors are costly, but proximate mechanisms mediating increased discriminative ability are unclear. We studied behavioral and neural mechanisms underlying responses to conspecific and heterospecific vocalizations in Alston’s singing mouse (Scotinomys teguina), a species in which males sing to repel rivals. We performed playback experiments using males in allopatry and sympatry with a dominant heterospecific (Scotinomys xerampelinus) and examined song-evoked induction of egr-1 in...

Polyethylene upcycling to long-chain alkylaromatics by tandem hydrogenolysis/aromatization

Fan Zhang, Manhao Zeng, Ryan Yappert, Jiakai Sun, Yu-Hsuan Lee, Anne LaPointe, Baron Peters, Mahdi Abu-Omar & Susannah Scott
The current scale of plastics production and the accompanying waste disposal problems represent a largely untapped opportunity for chemical upcycling. Tandem catalytic conversion by Pt/g-Al2O3 converts various polyethylene grades in high yields (up to 80 wt%) to low molecular-weight liquid/wax products, in the absence of added solvent or H2, with little production of light gases. The major components are valuable long-chain alkylaromatics and alkylnaphthenes (average ca. C30, Ð = 1.1). Coupling exothermic hydrogenolysis with endothermic...

Molecular assays of pollen use consistently reflect pollinator visitation patterns in a system of flowering plants

Aubrie James, Monica Geber & David Toews
Determining how pollinators visit plants versus how they carry and transfer pollen is an ongoing project in pollination ecology. The current tools for identifying the pollens that bees carry have different strengths and weaknesses when used for ecological inference. In this study we use three methods to better understand a system of congeneric, co-flowering plants in the genus Clarkia and their bee pollinators: observations of plant-pollinator contact in the field, and two different molecular methods...

Data from: Assessing avian diversity and community composition along a successional gradient in traditional Lacandon Maya agroforests

Tomasz B. Falkowski, José Raúl Vázquez Pérez, Adolfo Chankin, Atzin Campos, José Luis Rangel, Jonathan B. Cohen & Stewart A.W. Diemont
Evidence regarding the ability of agroforests to conserve biological diversity has been mixed; they tend to maintain avian communities with species richness similar to that of undisturbed forest ecosystems but generally do not completely preserve community composition. Using a combination of occupancy modeling and non-metric multidimensional scaling on point-count data, we assessed changes in avian community diversity and composition along a successional gradient in traditional Lacandon Maya agroforests and compared them to protected areas in...

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