129,792 Works

Phylogenetic signals in pest abundance and distribution range of spider mites

Peng-Yu Jin, Jing-Tao Sun, Ary Hoffmann, Yan-Fei Guo, Jin-Cheng Zhou, Yu-Xi Zhu, Lei Chen & Xiao-Yue Hong
Attributes of pest species like host range are frequently reported as being evolutionarily constrained and showing phylogenetic signal. Because these attributes in turn could influence the abundance and impact of species, phylogenetic information could be useful in predicting the likely status of pests. In this study, we used regional (China) and global datasets to investigate phylogenetic patterns in occurrence patterns and host ranges of spider mites, which constitute a pest group of many cropping systems...

Spectral-ratio tomography for attenuation estimation

Ziqi Jin
In the measurement of surface seismic data, an accurate attenuation-estimation method is necessary to compensate for the energy loss and phase distortion of seismic waves, and also beneficial for further quantitative amplitude analyses and reservoir parameters prediction. We design a more accurate Q tomography method to estimate Q values. This method inverts for the Q values in the overburden and target layer simultaneously without assumptions on the overburden, which allows us to separate the overburden...

Data from: Substrate stoichiometry determines nitrogen fixation throughout succession in southern Chinese forests

Mianhai Zheng, Hao Chen, Dejun Li, Yiqi Luo & Jiangming Mo
The traditional view holds that biological nitrogen (N) fixation often peaks in early- or mid-successional ecosystems and declines throughout succession based on the hypothesis that soil N richness and/or phosphorus (P) depletion become disadvantageous to N fixers. This view, however, fails to support the observation that N fixers can remain active in many old-growth forests despite the presence of N-rich and/or P-limiting soils. Here, we found unexpected increases in N fixation rates in the soil,...

Increased spatial-genetic structure in a population of the clonal aquatic plant Sagittaria latifolia (Alismataceae) following disturbance

Marcel Dorken, Ryan Holt & Allison Kwok
The spatial genetic structure (SGS) of plant populations is determined by the outcome of key ecological processes, including pollen and seed dispersal, the intensity of local resource competition among newly recruited plants, and patterns of mortality among established plants. Changes in the magnitude of SGS over time can provide insights into the operation of these processes. We measured SGS in a population of the clonal aquatic plant, Sagittaria latifolia that had been disturbed by flooding,...

Pre-closure fishing pressure predicts effects of marine protected areas

Erin Jaco & Mark Steele
1. Marine Protected Areas (MPAs) can be effective tools for marine resource management. However, despite evidence of the positive effects of MPAs, such as increases in body sizes of organisms targeted by fisheries, there is often heterogeneity in biological outcomes among them. 2. Because fishing can drastically impact fish populations, the goal of this study was to determine if the levels of exploitation prior to protection could predict variation in the magnitude of MPA effects....

Metabolomic Analysis of the Effects of Leptin Replacement Therapy in Patients with Lipodystrophy

Shivraj Grewal, Sriram Gubbi, Andin Fosam, Caroline Sedmak, Shanaz Sikder, Harsha Talluru, Rebecca Brown, Ranganath Muniyappa & Rebecca J Brown
Context and Objective Leptin treatment has dramatic clinical effects on glucose and lipid metabolism in leptin-deficient patients with lipodystrophy. Further elucidation of metabolic effects of exogenous leptin therapy will shed light on understanding leptin physiology in humans. Our objective was to utilize metabolomic profiling to examine the changes associated with administration of short-term metreleptin therapy in patients with lipodystrophy. Study Design We conducted a pre-post treatment study in 19 patients (75% female) with varying forms...

Data from: Contribution of European forests to safeguard wild honey bee populations

Fabrice Requier, Yoan Paillet, Fabien Laroche, Benjamin Rutschmann, Jie Zhang, Fabio Lombardi, Miroslav Svoboda & Ingolf Steffan-Dewenter
Recent studies reveal the use of tree cavities by wild honey bee colonies in European forests. This highlights the conservation potential of forests for a highly threatened component of the native entomofauna in Europe, but currently no estimate of potential wild honey bee population sizes exists. Here, we analysed the tree cavity densities of 106 forest areas across Europe and inferred an expected population size of wild honey bees. Both forest and management types affected...

Hybridization between Felis silvestris silvestris and Felis silvestris catus in two contrasted environments in France

Marie-Pauline Beugin, Olivier Savaldor, Guillaume Leblanc, Guillaume Queney, Eugenia Natoli & Domnique Pontier
European wildcat (Felis silvestris silvestris) populations are fragmented throughout most of the whole range of the sub-species, and may be threatened by hybridization with the domestic cat F.s. catus. The underlying ecological processes promoting hybridization, remain largely unknown. In France, wildcats are mainly present in the North-East and signs of their presence in the Pyrenees have been recently provided. However, no studies have been carried out in the French Pyrenees to assess their exposure to...

Ancient mitogenomics clarifies radiation of extinct Mascarene giant tortoises (Cylindraspis spp.)

Christian Kehlmaier, Eva Graciá, Patrick D. Campbell, Margaretha D. Hofmeyr, Silke Schweiger, Albert Martínez-Silvestre, Walter Joyce & Uwe Fritz
The five extinct giant tortoises of the genus Cylindraspis belong to the most iconic species of the enigmatic fauna of the Mascarene Islands that went largely extinct after the discovery of the islands. To resolve the phylogeny and biogeography of Cylindraspis, we analysed a data set of 45 mitogenomes that includes all lineages of extant tortoises and eight near-complete sequences of all Mascarene species extracted from historic and subfossil material. Cylindraspis is an ancient lineage...

Population history explains the performance of an annual herb - within and beyond its European species range

Jan Douda, Jana Doudová, Eva Hodková, Petr Vít, Karol Krak & Bohumil Mandák
1. The centre-periphery hypothesis (CPH) predicts a decrease in population performance from the centre of the species range towards the edge, hindering further species expansion. To overcome ecological limitation, local adaptation of peripheral populations is assumed necessary to extend niche space and thus to potentially facilitate species’ range expansion. However, adaptive changes do not necessarily correspond to current ecological marginality. Instead, population history may provide a fuller context for understanding patterns of local adaptation within...

Migrating bison engineer the green wave

Chris Geremia, Jerod Merkle, Daniel Eacker, Rick Wallen, P.J. White, Mark Hebblewhite & Matthew Kauffman
Newly emerging plants provide the best forage for herbivores. To exploit this fleeting resource, migrating herbivores align their movements to surf the wave of spring green-up. With new technology to track migrating animals, the Green Wave Hypothesis has steadily gained empirical support across a diversity of migratory taxa. This hypothesis assumes the green wave is controlled by variation in climate, weather, and topography, and its progression dictates the timing, pace, and extent of migrations. However,...

Herding mechanisms to maintain the cohesion of a harem group: two interaction phases during herding

Monamie Ringhofer, Clark Kendrick Go, Sota Inoue, Renata S. Mendonça, Satoshi Hirata, Takatomi Kubo, Kazushi Ikeda & Shinya Yamamoto
In animal groups, individual interactions achieve coordinated movements to maintain cohesion. In horse harem groups, herding is a behavior in which males chase females from behind; it is considered to assist with group cohesiveness. However, the mechanisms by which the individuals move to maintain group cohesion are unknown. We applied novel non-invasive methods of drone filming and video tracking to observe horse movements in the field with high temporal and spatial resolution. We tracked all...

Fire regimes and pollinator behavior explain the genetic structure of Puya hamata (Bromeliaceae) rosette plants

Rommel Montúfar
The demography of the Andean Puya hamata has been linked to fire regimes and hummingbird behaviour, which might modify the plant’s population genetic diversity. Naturally poor dispersal results in patches of genetically related plants, a pattern intensified further by burning which promotes seedling germination around parent plants. Later, when these plants flower, large patches are attractive to territorial hummingbirds which prevent visits by traplining hummingbird species, carrying pollen from likely unrelated plants. To explore this...

Macrophage coordination of the interferon lambda immune response

Scott Read
Lambda interferons (IFN-λs) are a major component of the innate immune defense to viruses, bacteria and fungi. In human liver, IFN-λ not only drives antiviral responses, but also promotes inflammation and fibrosis in viral and non-viral diseases. Here we demonstrate that macrophages are primary responders to IFN-λ, uniquely positioned to bridge the gap between IFN-λ producing cells and lymphocyte populations that are not intrinsically responsive to IFN-λ. While CD14+ monocytes do not express the IFN-λ...

Data from: Primary dermal fibroblasts and pectoralis muscle show similar patterns of oxidative stress in tropical and temperate birds despite differing life-histories

Ana Jimenez, Ursula Beattie & Haviland Wright
Tropical birds have a “slower pace of life,” with lower rates of whole-animal metabolism, smaller metabolically active organs, and lower cellular metabolic rates than their temperate counterparts. Oxidative stress is a physiological mechanism that may dictate differing life-histories such as those found between tropical and temperate birds. Oxygen is required to make ATP, resulting in the production of reactive oxygen species (ROS). If left unchecked, ROS can structurally alter proteins, induce mutations in DNA, and...

Numerical Simulations of Laboratory-Scale, Hypervelocity-Impact Experiments for Asteroid-Deflection Code Validation

Tane P. Remington, J. Michael Owen, Akiko M. Nakamura, Paul L. Miller & Megan B. Syal
Asteroids and comets have the potential to impact Earth and cause damage at the local to global scale. Deflection or disruption of a potentially hazardous object could prevent future Earth impacts, but due to our limited ability to perform experiments directly on asteroids, our understanding of the process relies upon large-scale hydrodynamic simulations. Related simulations must be vetted through code validation by benchmarking against relevant laboratory-scale hypervelocity-impact experiments. To this end, we compare simulation results...

Spatial sampling bias and model complexity in stream-based species distribution models: a case study of Paddlefish (Polyodon spathula) in the Arkansas River basin, U.S.A.

Andrew Taylor, Thomas Hafen, Colt Holley, Alin González & James Long
Leveraging existing presence records and geospatial datasets, species distribution modeling has been widely applied to informing species conservation and restoration efforts. Maxent is one of the most popular modeling algorithms, yet recent research has demonstrated Maxent models are vulnerable to prediction errors related to spatial sampling bias and model complexity. Despite elevated rates of biodiversity imperilment in stream systems, the application of Maxent models to stream networks has lagged, as has the availability of tools...

Data from: Strength of species interactions determines biodiversity and stability in microbial communities

Christoph Ratzke, Julien Barrere & Jeff Gore
Organisms, especially microbes, tend to live in complex communities. While some of these ecosystems are very bio-diverse, others aren′t, and while some are very stable over time others undergo strong temporal fluctuations. Despite a long history of research and a plethora of data it is not fully understood what sets biodiversity and stability of ecosystems. Theory as well as experiments suggest a connection between species interaction, biodiversity, and stability of ecosystems, where an increase of...

Rapid and predictable evolution of admixed populations between two Drosophila species pairs

Daniel Matute, Aaron Comeault, Eric Earley, Antonio Serrato-Capuchina, David Peede, Anaïs Monroy-Eklund, Wen Huang, Corbin Jones, Trudy Mackay & Jerry Coyne
The consequences of hybridization are varied, ranging from the origin of new lineages, introgression of some genes between species, to the extinction of one of the hybridizing species. We generated replicate admixed populations between two pairs of sister species of Drosophila: D. simulans and D. mauritiana; and D. yakuba and D. santomea. Each pair consisted of a continental species and an island endemic. The admixed populations were maintained by random mating in discrete generations for...

Cold-water coral assemblages on vertical walls: distribution patterns from the Northeast Atlantic

Katleen Robert
Aim: In this study, we assess patterns of cold-water coral assemblages observed on deep-sea vertical walls. Similar to their shallow-water counterparts, vertical and overhanging walls in the deep sea can host highly diverse communities, but because of their geometry, these habitats are generally overlooked and remain poorly known. These vertical habitats are however of particular interest, because they can protect vulnerable coral ecosystems from trawling activities. As such, it is important to understand their ecology...

Spectrum of mutational signatures in T-cell lymphoma reveals a key role for UV radiation in mycosis fungoides and Sezary syndrome

Christine Jones, Andrea Degasperi, Vieri Grandi, Tracey Mitchell & Serena Nik-Zainal
T-cell non-Hodgkin’s lymphomas (NHL) develop following transformation of tissue resident T-cells. We performed a meta-analysis of mutational catalogues derived from whole exome sequencing data from 403 patients with eight subtypes of T-cell NHL to identify mutational signatures and recurrent gene mutations associated with specific causal peaks within these signatures. Signature 1, indicative of age-related deamination, was prevalent across all T-cell NHL subtypes, reflecting the derivation of these malignancies from memory T-cell subsets. Adult T-cell leukemia-lymphoma...

The Burgess Shale paleocommunity with new insights from Marble Canyon, British Columbia

Karma Nanglu, Jean-Bernard Caron & Robert Gaines
The middle (Wuliuan Stage) Cambrian Burgess Shale is famous for its exceptional preservation of diverse and abundant soft-bodied animals through the “thick” Stephen Formation. However, with the exception of the Walcott Quarry (Fossil Ridge) and the stratigraphically older Tulip Beds (Mount Stephen) which are both in Yoho National Park (British Columbia), quantitative assessments of the Burgess Shale have remained limited. Here we first provide a detailed quantitative overview of the diversity and structure of the...

Data from: Phenotypic plasticity, but not adaptive tracking, underlies seasonal variation in post-cold hardening freeze tolerance of Drosophila melanogaster

Helen Stone, Priscilla Erickson & Alan Bergland
In temperate regions, an organism’s ability to rapidly adapt to seasonally varying environments is essential for its survival. In response to seasonal changes in selection pressure caused by variation in temperature, humidity, and food availability, some organisms exhibit plastic changes in phenotype. In other cases, seasonal variation in selection pressure can rapidly increase the frequency of genotypes that offer survival or reproductive advantages under the current conditions. Little is known about the relative influences of...

Data from: Comparative phylogeography of three host sea anemones in the Indo-Pacific

Pablo Saenz-Agudelo, Madeleine Emms, Emily Giles, Remy Gatins, Gerrit Nanninga, Anna Scott, Jean Paul Hobbs, Ashley Frisch, Suzanne Mills, Ricardo Beldade & Michael Berumen
Aim The mutualistic relationship between anemones and anemonefishes is one of the most iconic examples of symbiosis. However, while anemonefishes have been extensively studied in terms of genetic connectivity, such information is lacking entirely for host sea anemones. Here, we provide the first information on the broad-scale population structure and phylogeographic patterns of three species of host sea anemone, Heteractis magnifica, Stichodactyla mertensii, and Entacmaea quadricolor. We evaluate if there is concordance in genetic structure...

Data from: Mediterranean marine protected areas have higher biodiversity via increased evenness, not abundance

Shane Blowes, Jonathan Chase, Antonio Di Franco, Ori Frid, Nicholas Gotelli, Paolo Guidetti, Tiffany Knight, Felix May, Daniel McGlinn, Fiorenza Micheli, Enric Sala & Jonathan Belmaker
1. Protected areas are central to biodiversity conservation. For marine fish, marine protected areas (MPAs) often harbour more individuals, especially of species targeted by fisheries. But precise pathways of biodiversity change remain unclear. For example, how local-scale responses combine to affect regional biodiversity, important for managing spatial networks of MPAs, is not well known. Protection potentially influences three components of fish assemblages that determine how species accumulate with sampling effort and spatial scale: the total...

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