594 Works

Data from: Hungry for the queen: honeybee nutritional environment affects worker pheromone response in a life stage‐dependent manner

Alexander Walton, Adam G. Dolezal, Marit A. Bakken & Amy L. Toth
1.Animal nutritional state can profoundly affect behavior, including an individual's tendency to cooperate with others. We investigated how nutritional restriction at different life stages affects cooperative behavior in a highly social species, Apis mellifera honey bees. 2.We found that nutritional restriction affects a worker's queen pheromone response, a behavioral indicator of investment in group vs. individual reproduction. Nutritional restriction at the larval stage led to reduced ovary size and increased queen pheromone response, whereas nutritional...

Data from: Intra-population genomics in a model mutualist: population structure and candidate symbiosis genes under selection in Medicago truncatula

Michael A. Grillo, Stephane De Mita, Patricia V. Burke, Kathryn L.S. Solórzano-Lowell & Katy Denise Heath
Bottom-up evolutionary approaches, including geographically-explicit population genomic analyses, have the power to reveal the mechanistic basis of adaptation. Here we conduct a population genomic analysis in the model legume, Medicago truncatula, in order to characterize population genetic structure and identify symbiosis-related genes showing evidence of spatially-variable selection. Using RAD-seq, we generated over 26,000 SNPs from 191 accessions from within three regions of the native range in Europe. Results from STRUCTURE analysis identify 5 distinct genetic...

Data from: Miocene flooding events of western Amazonia

Carlos Jaramillo, Ingrid Romero, Carlos D'Apolito, German Bayona, Edward Duarte, Stephen Louwye, Jaime Escobar, Javier Luque, Jorge D. Carrillo-Briceño, Vladimir Zapata, Andrés Mora, Stefan Schouten, Michael Zavada, Guy Harrington, John Ortiz & Frank P. Wesselingh
There is a considerable controversy about whether western Amazonia was ever covered by marine waters during the Miocene [23 to 5 Ma (million years ago)]. We investigated the possible occurrence of Miocene marine incursions in the Llanos and Amazonas/Solimões basins, using sedimentological and palynological data from two sediment cores taken in eastern Colombia and northwestern Brazil together with seismic information. We observed two distinct marine intervals in the Llanos Basin, an early Miocene that lasted...

Data from: Adaptation to deep-sea chemosynthetic environments as revealed by mussel genomes

Jin Sun, Yu Zhang, Ting Xu, Yang Zhang, Huawei Mu, Yanjie Zhang, Yi Lan, Christopher J. Fields, Jerome H. L. Hui, Wei-Peng Zhang, Runsheng Li, Wenyan Nong, Fiona K. M. Cheung, Jian-Wen Qiu & Pei-Yuan Qian
Hydrothermal vents and methane seeps are extreme deep-sea ecosystems that support dense populations of specialised macrobenthos such as mussels. But lack of genome information hinders understanding of the adaptation of these animals to such inhospitable environment. Here we report the genomes of a deep-sea vent/seep mussel Bathymodiolus platifrons and a shallow-water mussel Modiolus philippinarum. Phylogenetic analysis shows that these mussel species diverged approximately 110.4 million years ago. Many gene families, especially those for stabilising protein...

Data from: Distinguishing migration events of different timing for wild boar in the Balkans

Panoraia Alexandri, Hendrik-Jan Megens, Richard P. M. A. Crooijmans, Martien A. M. Groenen, Daniel J. Goedbloed, Juan M. Herrero-Medrano, Lauretta A. Rund, Lawrence B. Schook, Evangelos Chatzinikos, Costas Triantaphyllidis, Alexandros Triantafyllidis, Laurence B. Schook & Alexander Triantafyllidis
Aim: We compared the power of different nuclear markers to investigate genetic structure of southern Balkan wild boar. We distinguished between historic events, such as isolation in different refugia during glacial periods, from recent demographic processes, such as naturally occurring expansions. Location: Southern Balkans/Greece. Methods: We sampled 555 wild boars from 20 different locations in southern Balkans/Greece. All individuals were analysed with 10 microsatellites and a subgroup of 91 with 49,508 single nucleotide polymorphisms (SNPs)....

Data from: The influence of spatial sampling scales on ant-plant interaction network architecture

Wesley Dáttilo, Jeferson Vizentin-Bugoni, Vanderlei J. Debastiani, Pedro Jordano & Thiago J. Izzo
1.Despite great interest in metrics to quantify the structure of ecological networks, the effects of sampling and scale remain poorly understood. In fact, one of the most challenging issues in ecology is how to define suitable scales (i.e., temporal or spatial) to accurately describe and understand ecological systems. 2.Here, we sampled a series of ant‐plant interaction networks in the southern Brazilian Amazon rainforest in order to determine whether the spatial sampling scale, from local to...

Data from: Evolution of the bamboos (Bambusoideae; Poaceae): a full plastome phylogenomic analysis

William P. Wysocki, Lynn G. Clark, Eduardo Ruiz-Sanchez, Lakshmi Attigala & Melvin R. Duvall
Background: Bambusoideae (Poaceae) comprise three distinct and well-supported lineages: tropical woody bamboos (Bambuseae), temperate woody bamboos (Arundinarieae) and herbaceous bamboos (Olyreae). Phylogenetic studies using chloroplast markers have generally supported a sister relationship between Bambuseae and Olyreae. This suggests either at least two origins of the woody bamboo syndrome in this subfamily or its loss in Olyreae. Results: Here a full chloroplast genome (plastome) phylogenomic study is presented using the coding and noncoding regions of 13...

Data from: Identification of the Minimal Cytolytic Unit for Streptolysin S and an Expansion of the Toxin Family

Evelyn M. Molloy, Sherwood R. Casajens, Courtney L. Cox, Tucker Maxson, Nicole A. Ethridge, Gabriele Margos, Volker Fingerle & Douglas A. Mitchell
Background: Streptolysin S (SLS) is a cytolytic virulence factor produced by the human pathogen Streptococcus pyogenes and other Streptococcus species. Related “SLS-like” toxins have been characterized in select strains of Clostridium and Listeria, with homologous clusters bioinformatically identified in a variety of other species. SLS is a member of the thiazole/oxazole-modified microcin (TOMM) family of natural products. The structure of SLS has yet to be deciphered and many questions remain regarding its structure-activity relationships. Results:...

Data from: The chemical basis of a signal of individual identity: Shell pigment concentrations track the unique appearance of Common Murre eggs

Mark E Hauber, Alexander L Bond, Amy-Lee Kouwenberg, Gregory J Robertson, Erpur S Hansen, Mande Holford, Miri Dainson, Alec Luro & James Dale
In group-living species with parental care, the accurate recognition of one’s own young is critical to fitness. Because discriminating offspring within a large colonial group may be challenging, progeny of colonial breeders often display familial or individual identity signals to elicit and receive costly parental provisions from their own parents. For instance, the Common Murre (or Common Guillemot: Uria aalge) is a colonially breeding seabird that does not build a nest and lays and incubates...

Data from: Rapid light-induced shifts in opsin expression: finding new opsins, discerning mechanisms of change, and implications for visual sensitivity

Rebecca C Fuller & Kristin M Claricoates
Light induced shifts in cone frequency and opsin expression occur in many aquatic species. Yet little is known about how quickly animals can alter opsin expression and, thereby, track their visual environments. Similarly, little is known about whether adult animals can alter opsin expression or whether shifts in opsin expression are limited to critical developmental windows. We took adult wild caught bluefin killifish (Lucania goodei) from three different lighting environments (spring, swamp, variable), placed them...

Data from: Historical population size change and differentiation of relict populations of the endangered giant kangaroo rat

Mark J. Statham, William T. Bean, Nathan Alexander, Michael F. Westphal & Benjamin N. Sacks
From a conservation management perspective it is important to understand how genetic diversity is partitioned across a species’ range, including (1) identification of evolutionarily distinct units versus those recently isolated through anthropogenic activities and (2) the relative genetic contributions among components of fragmented (meta)populations. To address these questions, we investigated the phylogeography and metapopulation structure among relict populations of the endangered giant kangaroo rat (Dipodomys ingens) in the highly altered San Joaquin Desert Ecosystem. This...

Data from: Paternal care in a fish: epigenetics and fitness enhancing effects on offspring anxiety

Katie E. McGhee & Alison M. Bell
In many animals, including humans, interactions with caring parents can have long-lasting effects on offspring sensitivity to stressors. However, whether these parental effects impact offspring fitness in nature is often unclear. In addition, despite evidence that maternal care can influence offspring behaviour via epigenetic alterations to the genome, it remains unclear whether paternal care has similar effects. Here, we show in three-spined sticklebacks, a fish in which fathers are the sole provider of offspring care,...

Data from: Colonization history and population differentiation of the Honey Bees (Apis mellifera L.) in Puerto Rico

Jenny P. Acevedo-Gonzalez, Alberto Galindo-Cardona, Arian Avalos, Charles W. Whitfield, Dania M. Rodriguez, Jose L. Uribe-Rubio & Tugrul Giray
Honey bees (Apis mellifera L.) are the primary commercial pollinators across the world. The subspecies A. m. scutellata originated in Africa and was introduced to the Americas in 1956. For the last 60 years it hybridized successfully with European subspecies, previous residents in the area. The result of this hybridization was called Africanized Honey Bee (AHB). AHB has spread since then, arriving to Puerto Rico (PR) in 1994. The honey bee population on the island...

Data from: The evolution of locomotor rhythmicity in tetrapods

Callum F. Ross, Richard W. Blob, David R. Carrier, Monica A. Daley, Stephen M. Deban, Brigitte Demes, Janaya L. Gripper, Jose Iriarte-Diaz, Brandon Michael Kilbourne, Tobias Landberg, John D. Polk, Nadja Schilling & Bieke Vanhooydonck
Differences in rhythmicity (relative variance in cycle period) between mammal, fish, and lizard feeding systems have been hypothesized to be associated with differences in their sensorimotor control systems. We tested this hypothesis by examining whether the locomotion of tachymetabolic tetrapods (birds and mammals) is more rhythmic than that of bradymetabolic tetrapods (lizards, alligators, turtles, salamanders). Species averages of intra-individual coefficients of variation in cycle period were compared while controlling for gait and substrate. Variance in...

Data from: Rates of genomic divergence in humans, chimpanzees and their lice

Kevin P. Johnson, Julie M. Allen, Brett P. Olds, Lawrence Mugisha, David L. Reed, Ken N. Paige & Barry R. Pittendrigh
The rate of DNA mutation and divergence is highly variable across the tree of life. However, the reasons underlying this variation are not well understood. Comparing the rates of genetic changes between hosts and parasite lineages that diverged at the same time is one way to begin to understand differences in genetic mutation and substitution rates. Such studies have indicated that the rate of genetic divergence in parasites is often faster than that of their...

Data from: Co-occurring expression and methylation QTLs allow detection of common causal variants and shared biological mechanisms

Brandon L. Pierce, Lin Tong, Maria Argos, Kathryn Demanelis, Farzana Jasmine, Muhammad Rakibuz-Zaman, Golam Sarwarq, , Hasan Shahriar, Tariqul Islam, Mahfuzar Rahman, , Muhammad G. Kibriya, Lin S. Chen & Habibul Ahsan
Inherited genetic variation affects local gene expression and DNA methylation in humans. Most expression quantitative trait loci (cis-eQTLs) occur at the same genomic location as methylation QTLs (cis-meQTLs), suggesting a common causal variant and shared mechanism. Using DNA and RNA from peripheral blood of Bangladeshi individuals, here we use co-localization methods to identify eQTL-meQTL pairs likely to share a causal variant. We use partial correlation and mediation analyses to identify >400 of these pairs showing...

Data from: Elevated CO2 and temperature increase soil C losses from a soybean-maize ecosystem

Christopher K. Black, Sarah C. Davis, Tara W. Hudiburg, Carl J. Bernacchi & Evan H. DeLucia
Warming temperatures and increasing CO2 are likely to have large effects on the amount of carbon stored in soil, but predictions of these effects are poorly constrained. We elevated temperature (canopy: +2.8 °C; soil growing season: +1.8 °C; soil fallow: +2.3 °C) for 3 years within the 9th–11th years of an elevated CO2 (+200 ppm) experiment on a maize–soybean agroecosystem, measured respiration by roots and soil microbes, and then used a process-based ecosystem model (DayCent)...

Data from: Integrating phylogenomic and population genomic patterns in avian lice provides a more complete picture of parasite evolution

Andrew D. Sweet, Bret M. Boyd, Julie M. Allen, Scott M. Villa, Michel P. Valim, Jose L. Rivera-Parra, Robert E. Wilson & Kevin P. Johnson
Parasite diversity accounts for most of the biodiversity on earth, and is shaped by many processes (e.g. cospeciation, host-switching). To identify the effects of the processes that shape parasite diversity, it is ideal to incorporate both deep (phylogenetic) and shallow (population) perspectives. To this end, we developed a novel workflow to obtain phylogenetic and population genetic data from whole genome sequences of body lice parasitizing New World ground-doves. Phylogenies from these data showed consistent, highly...

Data from: Genomic basis of life history evolution in Drosophila melanogaster

Silvia C. Remolina, Peter L. Chang, Jeff Leips, Sergey V. Nuzhdin & Kimberly A. Hughes
Natural diversity in aging and other life history patterns is a hallmark of organismal variation. Related species, populations, and individuals within populations show genetically based variation in life span and other aspects of age-related performance. Population differences are especially informative because these differences can be large relative to within-population variation and because they occur in organisms with otherwise similar genomes. We used experimental evolution to produce populations divergent for life span and late-age fertility and...

Data from: The evolutionary history of dogs in the Americas

Máire Ní Leathlobhair, Angela R. Perri, Evan K. Irving-Pease, Kelsey E. Witt, Anna Linderholm, James Haile, Ophelie Lebrasseur, Carly Ameen, Jeffrey Blick, Adam R. Boyko, Selina Brace, Yahaira Nunes Cortes, Susan J. Crockford, Alison Devault, Evangelos A. Dimopoulos, Morley Eldridge, Jacob Enk, Shyam Gopalakrishnan, Kevin Gori, Vaughan Grimes, Eric Guiry, Anders J. Hansen, Ardern Hulme-Beaman, John Johnson, Andrew Kitchen … & Laurent A. F. Frantz
Dogs were present in the Americas prior to the arrival of European colonists, but the origin and fate of these pre-contact dogs are largely unknown. We sequenced 71 mitochondrial and seven nuclear genomes from ancient North American and Siberian dogs spanning ~9,000 years. Our analysis indicates that American dogs were not domesticated from North American wolves. Instead, American dogs form a monophyletic lineage that likely originated in Siberia and dispersed into the Americas alongside people....

Data from: Root volume distribution of maturing perennial grasses revealed by correcting for minirhizotron surface effects

Christopher K. Black, Michael D. Masters, David S. LeBauer, Kristina J. Anderson-Teixeira & Evan H. DeLucia
Aims: Root architecture drives plant ecology and physiology, but current detection methods limit understanding of root placement within soil profiles. We developed a statistical model of root volume along depth gradients and used it to infer carbon storage potential of land-use changes from conventional agriculture to perennial bioenergy grasses. Methods: We estimated root volume of maize-soybean rotation and three perennial grass systems (Miscanthus × giganteus, Panicum virgatum, tallgrass prairie mix) by Bayesian modeling from minirhizotron...

Data from: Brazilian sugarcane ethanol as an expandable green alternative to crude oil use

Deepak Jaiswal, Amanda P. De Souza, Søren Larsen, David S. LeBauer, Fernando E. Miguez, Gerd Sparovek, Germán Bollero, Marcos S. Buckeridge & Stephen P. Long
Reduction of CO2 emissions will require a transition from fossil fuels to alternative energy sources. Expansion of Brazilian sugarcane ethanol1, 2 provides one near-term scalable solution to reduce CO2 emissions from the global transport sector. In contrast to corn ethanol, the Brazilian sugarcane ethanol system may offset 86% of CO2 emissions compared to oil use, and emissions resulting from land-use change to sugarcane are paid back in just 2–8 years3, 4. But, it has been...

Data from: Global metabolic interaction network of the human gut microbiota for context-specific community-scale analysis

Jaeyun Sung, Seunghyeon Kim, Josephine Jill T. Cabatbat, Sungho Jang, Yong-Su Jin, Gyoo Yeol Jung, Nicholas Chia & Pan-Jun Kim
A system-level framework of complex microbe–microbe and host–microbe chemical cross-talk would help elucidate the role of our gut microbiota in health and disease. Here we report a literature-curated interspecies network of the human gut microbiota, called NJS16. This is an extensive data resource composed of ∼570 microbial species and 3 human cell types metabolically interacting through >4,400 small-molecule transport and macromolecule degradation events. Based on the contents of our network, we develop a mathematical approach...

Data from: Anthropogenic ecosystem disturbance and the recovery debt

David Moreno Mateos, Edward B. Barbier, Peter C. Jones, Holly P. Jones, James Aronson, Jose A. Lopez-Lopez, Michelle L. McCrackin, Paula Meli, Daniel Montoya & José Rey Benayas
Ecosystem recovery from anthropogenic disturbances, either without human intervention or assisted by ecological restoration, is increasingly occurring worldwide. As ecosystems progress through recovery, it is important to estimate any resulting deficit in biodiversity and functions. Here we use data from 3,035 sampling plots worldwide, to quantify the interim reduction of biodiversity and functions occurring during the recovery process (that is, the ‘recovery debt’). Compared with reference levels, recovering ecosystems run annual deficits of 46–51% for...

Data from: Wnt/PCP controls spreading of Wnt/β-catenin signals by cytonemes in vertebrates

Benjamin Mattes, Yonglong Dang, Gediminas Greicius, Lilian Tamara Kaufmann, Benedikt Prunsche, Jakob Rosenbauer, Johannes Stegmaier, Ralf Mikut, Suat Özbek, Gerd Ulrich Nienhaus, Alexander Schug, David M. Virshup & Steffen Scholpp
Signaling filopodia, termed cytonemes, are dynamic actin-based membrane structures that regulate the exchange of signaling molecules and their receptors within tissues. However, how cytoneme formation is regulated remains unclear. Here, we show that Wnt/PCP autocrine signaling controls the emergence of cytonemes, and that cytonemes subsequently control paracrine Wnt/β-catenin signal activation. Upon binding of the Wnt family member Wnt8a, the receptor tyrosine kinase Ror2 gets activated. Ror2/PCP signaling leads to induction of cytonemes, which mediate transport...

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