352 Works

The evolution of reproductive isolation in Daphnia

Tiffany Chin, Carla E. Cáceres & Melania E. Cristescu
Background The process by which populations evolve to become new species involves the emergence of various reproductive isolating barriers (RIB). Despite major advancements in understanding this complex process, very little is known about the order in which RIBs evolve or their relative contribution to the total restriction of gene flow during various stages of speciation. This is mainly due to the difficulties of studying reproductive isolation during the early stages of species formation. This study...

Communities that thrive in extreme conditions captured from a freshwater lake

Etienne Low-Decarie, Gregor F. Fussmann, Alex J. Dumbrell & Graham Bell
Organisms that can grow in extreme conditions would be expected to be confined to extreme environments. However, we were able to capture highly productive communities of algae and bacteria capable of growing in acidic (pH 2), basic (pH 12) and saline (40 ppt) conditions from an ordinary freshwater lake. Microbial communities may thus include taxa that are highly productive in conditions that are far outside the range of conditions experienced in their host ecosystem. The...

Data from: Unveiling the food webs of tetrapods across Europe through the prism of the Eltonian niche

Louise O'Connor, Laura J. Pollock, João Braga, Gentile Francesco Ficetola, Alessandro Montemaggiori, Luigi Maiorano, Wilfried Thuiller, Marc Ohlmann & Camille Martinez-Almoyna
Aim Despite the recent calls on integrating the interaction networks into the study of large‐scale biodiversity patterns, we still lack a basic understanding of the functional characteristics of large interaction networks and how they are structured across environments. Here, building on recent advances in network science around the Eltonian niche concept, we aim to characterize the trophic groups in a large food web, and understand how these trophic groups vary across space. Location Europe and...

Data from: Repeatability of adaptive radiation depends on spatial scale: regional versus global replicates of stickleback in lake versus stream habitats

Antoine Paccard, Dieta Hanson, Yoel E Stuart, Frank A Von Hippel, Martin Kalbe, Tom Klepaker, Skúli Skúlason, Bjarni K Kristjánsson, Daniel I Bolnick, Andrew P Hendry & Rowan D H Barrett
The repeatability of adaptive radiation is expected to be scale dependent, with determinism decreasing as greater spatial separation among “replicates” leads to their increased genetic and ecological independence. Threespine stickleback (Gasterosteus aculeatus) provide an opportunity to test whether this expectation holds for the early stages of adaptive radiation -their diversification in freshwater ecosystems has been replicated many times. To better understand the repeatability of that adaptive radiation, we examined the influence of geographic scale on...

Data from: Linking a mutation to survival in wild mice

Rowan D. H. Barrett, Stefan Laurent, Ricardo Mallarino, Susanne P. Pfeifer, Charles C. Y. Xu, Matthieu Foll, Kazumasa Wakamatsu, Jonathan S. Duke-Cohan, Jeffrey D. Jensen & Hopi E. Hoekstra
Adaptive evolution in new or changing environments can be difficult to predict because the functional connections between genotype, phenotype, and fitness are complex. Here, we make these explicit connections by combining field and laboratory experiments in wild mice. We first directly estimate natural selection on pigmentation traits and an underlying pigment locus, Agouti, by using experimental enclosures of mice on different soil colors. Next, we show how a mutation in Agouti associated with survival causes...

Data from: Behavioral classification of low frequency acceleration and temperature data from a free ranging small mammal

Emily K. Studd, Manuelle Landry-Cuerrier, Allyson K. Menzies, Stan Boutin, Andrew G. McAdam, Jeffrey E. Lane & Murray M. Humphries
1. The miniaturization and affordability of new technology is driving a biologging revolution in wildlife ecology with use of animal-borne data logging devices. Among many new biologging technologies, accelerometers are emerging as key tools for continuously recording animal behavior. Yet a critical, but under-acknowledged consideration in biologging is the trade-off between sampling rate and sampling duration, created by battery- (or memory-) related sampling constraints. This is especially acute among small animals, causing most researchers to...

Data from: Is biasing offspring sex ratio adaptive? a test of Fisher’s principle across multiple generations of a wild mammal in a fluctuating environment

Andrea E. Wishart, Cory T. Williams, Andrew G. McAdam, Stan Boutin, Ben Dantzer, Murray M. Humphries, Dave W. Coltman, Jeffrey E. Lane & David W. Coltman
Fisher’s principle explains that population sex ratio in sexually reproducing organisms is maintained at 1:1 due to negative frequency-dependent selection, such that individuals of the rare sex realize greater reproductive opportunity than individuals of the more common sex until equilibrium is reached. If biasing offspring sex ratio towards the rare sex is adaptive, individuals that do so should have a higher number of grandoffspring. In a wild population of North American red squirrels (Tamiasciurus hudsonicus)...

A global meta-analysis of temperature effects on marine fishes’ digestion across trophic groups

Nicole Knight, Frederic Guichard & Andrew Altieri
Aim: The temperature constraint hypothesis proposes that marine herbivorous fishes are rare at high latitudes relative to carnivorous fishes because low temperatures impair the digestion of plant material. To test this hypothesis, we compared the effects of temperature on the digestive performance and investment of marine fishes across trophic groups. Location: Global marine ecosystems. Major Taxa Studied: Marine fishes. Methods: We analyzed data from 304 species consuming a range of diets to quantify the effects...

Data from: Noradrenergic projections from the locus coeruleus to the amygdala constrain fear memory reconsolidation

Josué Haubrich, Matteo Bernabo & Karim Nader
Memory reconsolidation is a fundamental plasticity process in the brain that allows established memories to be changed or erased. However, certain boundary conditions limit the parameters under which memories can be made plastic. Strong memories do not destabilize, for instance, although why they are resilient is mostly unknown. Here, we extend the understanding of the mechanisms implicated in reconsolidation-resistant memories by investigating the hypothesis that specific modulatory signals shape memory formation into a state that...

Fish mock community with 41 species from 13 orders

Jose Sergio Hleap, Joanne E. Littlefair, Dirk Steinke, Paul D. N. Hebert & Melania E. Cristescu
Tissue extracts of 41 North American fish species were obtained from the Ministère des Forêts, de la Faune et des Parcs (Québec). The selected species were chosen to represent a diversity of families within the Actinopterygii, and to include some species known to be present at the Experimental Lakes Area. Muscle or fin tissue was extracted using Qiagen Blood and Tissue kits and equimolarised to 15ng/µl. Library preparation and next-generation sequencing (NGS) was performed by...

Environmental drivers of Sphagnum growth in peatlands across the Holarctic region

Fia Bengtsson, Håkan Rydin, Jennifer Baltzer, Luca Bragazza, Zhao-Jun Bu, Simon Caporn, Ellen Dorrepaal, Kjell Ivar Flatberg, Olga Galanina, Mariusz Gałka, Anna Ganeva, Irina Goia, Nadezhda Goncharova, Michal Hajek, Akira Haraguchi, Lorna Harris, Elyn Humphreys, Martin Jiroušek, Katarzyna Kajukało, Edgar Karofeld, Natalia Koronatova, Natalia Kosykh, Anna Laine, Mariusz Lamentowicz, Elena Lapshina … & Richard J. Payne
The relative importance of global versus local environmental factors for growth and thus carbon uptake of the bryophyte genus Sphagnum – the main peat-former and ecosystem engineer in northern peatlands – remains unclear. 2) We measured length growth and net primary production (NPP) of two abundant Sphagnum species across 99 Holarctic peatlands. We tested the importance of previously proposed abiotic and biotic drivers for peatland carbon uptake (climate, N deposition, water table depth, and vascular...

Adding the third dimension to studies of parallel evolution of morphology and function: an exploration based on parapatric lake-stream stickleback

Grant Haines, Yoel Stuart, Dieta Hanson, Tania Tasneem, Daniel Bolnick, Hans Larsson & Andrew Hendry
Recent methodological advances have led to a rapid expansion of evolutionary studies employing three-dimensional landmark-based geometric morphometrics (GM). GM methods generally enable researchers to capture and compare complex shape phenotypes, and to quantify their relationship to environmental gradients. However, some recent studies have shown that the common, inexpensive, and relatively rapid two-dimensional GM methods can distort important information and produce misleading results because they cannot capture variation in the depth (Z) dimension. We use micro-CT...

Effect of the Central American Isthmus on gene flow and divergence of the American crocodile Crocodylus acutus

Jose Avila-Cervantes, Carlos Arias, Miryam Venegas-Anaya, Marta Vargas, Hans C. E. Larsson & W. Owen McMillan
The final formation of the Central American Isthmus (CAI) about 3.5 Ma altered global ocean circulation, connected North and South America terrestrial biotas and established the Caribbean Sea. The nature of this event creates a natural scenario to test vicariance, divergence, and speciation by allopatry. Studies have shown the effect of the CAI on marine and terrestrial species, but none have examined a large-bodied amphibious taxon. We used RAD sequencing on populations of the American...

Genetic and phenotypic diversity of guppy population pre- and post-flood disturbance

Léa Blondel
Rare extreme “black swan” disturbances can impact ecosystems in many ways, such as destroying habitats, depleting resources, and causing high mortality. In rivers, for instance, exceptional floods that occur infrequently (e.g., so-called “50-year floods”) can strongly impact the abundance of fishes and other aquatic organisms. Beyond such ecological effects, these floods could also impact intraspecific diversity by elevating genetic drift or dispersal and by imposing strong selection, which could then influence the population’s ability to...

Data from: Habitat disturbance alters color contrast and the detectability of cryptic and aposematic frogs

James Barnett, Brandon Varela, Ben Jennings, David Lesbarrères, Jonathan Pruitt & David Green
Animals use color both to conceal and signal their presence, with patterns that match the background, disrupt shape recognition, or highlight features important for communication. The forms that these color patterns take are responses to the visual systems that observe them and the environments within which they are viewed. Increasingly, however, these environments are being affected by human activity. We studied how pattern characteristics and habitat change may affect the detectability of three frog color...

Sexual maturity in Barn Owl (Tyto alba)

Paul Béziers & Alexandre Roulin
The age at first reproduction can significantly impact fitness. We investigated the possible source of variation in the age at first reproduction (“sexual maturity”) and its consequences for lifetime reproductive success in a wild population of barn owls. This raptor is sexually dimorphic for two melanin-based plumage traits shown to covary with sex-specific behaviour and physiology. We observed that females were sexually mature earlier than males, an effect that depended on the colour of their...

Data from: Vertebrate scavenging dynamics differ between carnivore and herbivore carcasses in the northern boreal forest

Michael Peers, Sean Konkolics, Yasmine Majchrzak, Allyson Menzies, Emily Studd, Rudy Boonstra, Stan Boutin & Clayton Lamb
Vertebrate scavenging can impact food web dynamics, but our understanding of this process stems predominantly from monitoring herbivore carrion and extrapolating results across carcass types. Recent evidence suggests carnivores may avoid intraguild scavenging to reduce parasite transmission. If this behavior is widespread across diverse ecosystems, estimation of nutrient cycling and community scavenging rates are likely biased to a currently unknown degree. We examined whether the time to initiate scavenging, carcass persistence, or the richness of...

SolCAP 8K array genotyping of population 15143

Helen Tai, Sai Reddy Achakkagari, Maria Kyriakidou, Kyle Gardner, David De Koeyer, Hielke De Jong & Martina Stromvik
The dataset is a tab-deliminted text file with genotyping information for a diploid potato progeny population derived from a cross of diploid potato clones 12120-03 X 07506-01. The SolCap 8303 Infinium Chip was used for SNP genotyping. It was originally generated for study on genetic mapping of Verticillium wilt resistance. The data was used again for analysis of segregation distortion in the most recent manuscript.

Data supporting: Environmental RNA degrades more rapidly than environmental DNA across a broad range of pH conditions

Kaushar Kagzi, Robert Hechler, Gregor Fussmann & Melania Cristescu
Although the use and development of molecular biomonitoring tools based on environmental nucleic acids (eDNA and eRNA; collectively known as eNAs) have gained broad interest for the quantification of biodiversity in natural ecosystems, studies investigating the impact of site-specific physicochemical parameters on eNA-based detection methods (particularly eRNA) remain scarce. Here, we used a controlled laboratory microcosm experiment to comparatively assess the environmental degradation of eDNA and eRNA across an acid-base gradient following complete removal of...

Paleolimnological assessment of a hyper-eutrophic lake (Nowlans Lake, N.S., Canada) Cladoceran communities

Abbie Gail Jones, Andrew Labaj, Julia Campbell, Nell Libera & Joshua Kurek
Mink fur farming was once a widespread agricultural activity in southwestern Nova Scotia. Some freshwaters near mink fur farm operations now show severe water quality issues. Notably, the watershed of Nowlans Lake (southwestern Nova Scotia, Canada) once contained six mink farms as well as a fish meal feed processing plant. It is now one of the most productive lakes in Atlantic Canada, with exceedingly high measured Total Phosphorus concentrations. Here, we provide data from a...

Publication release: How well do species distribution models predict occurrences in exotic ranges?

Dat Nguyen & Brian Leung
Species distribution models (SDMs) are widely used predictive tools to forecast potential biological invasions. However, the reliability of SDMs extrapolated to exotic ranges remains understudied, with most analyses restricted to few species and equivocal results. We examined the spatial transferability of SDMs for 647 non-indigenous species extrapolated across 1,867 invaded ranges, and identify what factors may help differentiate predictive success from failure. We performed a large-scale assessment of the transferability of SDMs using two modelling...

Scale-dependent environmental effects on phenotypic distributions in Heliconius butterflies

Ananda Regina Pereira Martins, Lucas Pereira Martins, Wing-Zheng Ho, W. Owen McMillan, Jonathan S. Ready & Rowan Barrett
Examining how environmental factors influence phenotypic distribution might provide valuable information about local adaptation, divergence, and speciation. The red-yellow Müllerian mimicry ring of Heliconius butterflies displays a wide range of color patterns across the Neotropics and is involved in several hybrid zones, making it an excellent system to study color phenotypic distribution. Using a multiscale distribution strategy, we studied whether different phenotypes of the distantly related species H. erato and H. melpomene, belonging to the...

Additional file 6 of Identification of SSBP1 as a ferroptosis-related biomarker of glioblastoma based on a novel mitochondria-related gene risk model and in vitro experiments

Jun Su, Yue Li, Qing Liu, Gang Peng, Chaoying Qin & Yang Li
Additional file 6: Table S1. The mitochondria-related genes extracted from the uniprot database.

Additional file 8 of Identification of SSBP1 as a ferroptosis-related biomarker of glioblastoma based on a novel mitochondria-related gene risk model and in vitro experiments

Jun Su, Yue Li, Qing Liu, Gang Peng, Chaoying Qin & Yang Li
Additional file 8: Table S3. The 201 DE-MRGs between neoplatstic and non-neoplastic cells.

Data from: Phylogenetic conservatism in plant phenology

T. Jonathan Davies, Elizabeth M. Wolkovich, Nathan J. B. Kraft, Nicolas Salamin, Jenica M. Allen, Toby R. Ault, Julio L. Betancourt, Kjell Bolmgren, Elsa E. Cleland, Benjamin I. Cook, Theresa M. Crimmins, Susan J. Mazer, Gregory J. McCabe, Stephanie Pau, Jim Regetz, Mark D. Schwartz & Steven E. Travers
Phenological events – defined points in the life cycle of a plant or animal – have been regarded as highly plastic traits, reflecting flexible responses to various environmental cues. The ability of a species to track, via shifts in phenological events, the abiotic environment through time might dictate its vulnerability to future climate change. Understanding the predictors and drivers of phenological change is therefore critical. Here, we evaluated evidence for phylogenetic conservatism – the tendency...

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