35 Works

Data from: Optimisation of next generation sequencing transcriptome annotation for species lacking sequenced genomes

Nina F. Ockendon, Lauren A. O'Connell, Stephen J. Bush, Jimena Monzon-Sandoval, Holly Barnes, Tamás Székely, Hans A. Hofmann, Steve Dorus & Araxi O. Urrutia
Next generation sequencing methods, such as RNA-seq, have permitted the exploration of gene expression in a range of organisms which have been studied in ecological contexts but lack a sequenced genome. However, the efficacy and accuracy of RNA-seq annotation methods using reference genomes from related species have yet to be robustly characterised. Here we conduct a comprehensive power analysis employing RNA-seq data from Drosophila melanogaster in conjunction with 11 additional genomes from related Drosophila species...

Data from: Heritable differences in fitness-related traits among populations of the mustard hill coral, Porites astreoides

Carly D. Kenkel, Samantha P. Setta & Mikhail V. Matz
A population’s potential for rapid evolutionary adaptation can be estimated from the amount of genetic variation in fitness-related traits. Inshore populations of the mustard hill coral (Porites astreoides) have been shown to be more tolerant to thermal stress than offshore populations, but it is unclear whether this difference is due to long-term physiological acclimatization or genetic adaptation. Here, we evaluated variation in growth rate and survival among 38 families of juvenile recruits of P. astreoides...

Data from: Genome-wide association study of Arabidopsis thaliana identifies determinants of natural variation in seed oil composition

Sandra E. Branham, Sara J. Wright, Aaron Reba & C. Randal Linder
The renewable source of highly reduced carbon provided by plant triacylglycerols (TAGs) fills an ever increasing demand for food, biodiesel, and industrial chemicals. Each of these uses requires different compositions of fatty acid proportions in seed oils. Identifying the genes responsible for variation in seed oil composition in nature provides targets for bioengineering fatty acid proportions optimized for various industrial and nutrition goals. Here, we characterized the seed oil composition of 391 world-wide, wild accessions...

Data from: Multimodal cues improve prey localization under complex environmental conditions

Flor Rhebergen, Ryan C. Taylor, Michael J. Ryan, Rachel A. Page & Wouter Halfwerk
Predators often eavesdrop on sexual displays of their prey. These displays can provide multimodal cues that aid predators, but the benefits in attending to them should depend on the environmental sensory conditions under which they forage. We assessed whether bats hunting for frogs use multimodal cues to locate their prey and whether their use varies with ambient conditions. We used a robotic set-up mimicking the sexual display of a male túngara frog (Physalaemus pustulosus) to...

Data from: Plastid genome sequences of legumes reveal parallel inversions and multiple losses of rps16 in papilionoids

Erika N. Schwarz, Tracey A. Ruhlman, Jamal S. M. Sabir, Nahid H. Ajarah, Njud S. Alharbi, Abdulrahman L. Al-Malki, C. Donovan Bailey, Robert K. Jansen & Nahid H. Hajrah
To date, publicly available plastid genomes of legumes have for the most part been limited to the subfamily Papilionoideae. Here we report 13 new plastid genomes of legumes spanning all three subfamilies. The genomes representing Caesalpinioideae and Mimosoideae are highly conserved in gene content and gene order, similar to the ancestral angiosperm genome organization. Genomes within the Papilionoideae, however, have reduced sizes due to deletions in nine intergenic spacers primarily in the large single copy...

Data from: Modeling character change heterogeneity in phylogenetic analyses of morphology through the use of priors

April M. Wright, Graeme T. Lloyd & David M. Hillis
The Mk model was developed for estimating phylogenetic trees from discrete morphological data, whether for living or fossil taxa. Like any model, the Mk model makes a number of assumptions. One assumption is that transitions between character states are symmetric (i.e., the probability of changing from 0 to 1 is the same as 1 to 0). However, some characters in a data matrix may not satisfy this assumption. Here, we test methods for relaxing this...

Data from: Population-specific covariation between immune function and color of nesting male threespine stickleback

Daniel I. Bolnick, Kum Chuan Shim, Matthew Schmerer & Chad D. Brock
Multiple biological processes can generate sexual selection on male visual signals such as color. For example, females may prefer colorful males because those males are more readily detected (perceptual bias), or because male color conveys information about male quality and associated direct or indirect benefits to females. For example, male threespine stickleback often exhibit red throat coloration, which females prefer both because red is more visible in certain environments, and red color is correlated with...

Data from: Open-ocean fish reveal an omnidirectional solution to camouflage in polarized environments

Parrish C. Brady, Alexander A. Gilerson, George W. Kattawar, James M. Sullivan, Michael S. Twardowski, Heidi M. Dierssen, Meng Gao, Kort Travis, Robert I. Etheredge, Alberto Tonizzo, Amir Ibrahim, Carlos Carrizo, Yalong Gu, Brandon J. Russell, Kathryn Mislinski, Shulei Zhao & Molly E. Cummings
Despite appearing featureless to our eyes, the open ocean is a highly variable environment for polarization-sensitive viewers. Dynamic visual backgrounds coupled with predator encounters from all possible directions make this habitat one of the most challenging for camouflage. We tested open-ocean crypsis in nature by collecting more than 1500 videopolarimetry measurements from live fish from distinct habitats under a variety of viewing conditions. Open-ocean fish species exhibited camouflage that was superior to that of both...

Data from: A tale of the ciliate tail: investigation into the adaptive significance of this sub-cellular structure

Brad J. Gemmell, Houshuo Jiang & Edward J. Buskey
Ciliates can form an important link between the microbial loop and higher trophic levels primarily through consumption by copepods. This high predation pressure has resulted in a number of ciliate species developing rapid escape swimming behaviour. Several species of these escaping ciliates also possess a long contractile tail for which the functionality remains unresolved. We use high-speed video, specialized optics and novel fluid visualization tools to evaluate the role of this contractile appendage in two...

Data from: Complete plastome sequence of Thalictrum coreanum (Ranunculaceae) and transfer of the rpl32 gene to the nucleus in the ancestor of the subfamily Thalictroideae

Seongjun Park, Robert K. Jansen & Seon Joo Park
Background: Plastids originated from cyanobacteria and the majority of the ancestral genes were lost or functionally transferred to the nucleus after endosymbiosis. Comparative genomic investigations have shown that gene transfer from plastids to the nucleus is an ongoing evolutionary process but molecular evidence for recent functional gene transfers among seed plants have only been documented for the four genes accD, infA, rpl22, and rpl32. Results: The complete plastid genome of Thalictrum coreaum, the first from...

Data from: The relationship between dN/dS and scaled selection coefficients

Stephanie J. Spielman & Claus O. Wilke
Numerous computational methods exist to assess the mode and strength of natural selection in protein-coding sequences, yet how distinct methods relate to one another remains largely unknown. Here, we elucidate the relationship between two widely-used phylogenetic modeling frameworks: dN/dS models and mutation-selection (MutSel) models. We derive a mathematical relationship between dN/dS and scaled selection coefficients, the focal parameters of MutSel models, and use this relationship to gain deeper insight into the behaviors, limitations, and applicabilities...

Data from: How does ascertainment bias in SNP analyses affect inferences about population history?

Emily Jane McTavish & David M. Hillis
Background: The selection of variable sites for inclusion in genomic analyses can influence results, especially when exemplar populations are used to determine polymorphic sites. We tested the impact of ascertainment bias on the inference of population genetic parameters using empirical and simulated data representing the three major continental groups of cattle: European, African, and Indian. We simulated data under three demographic models. Each simulated data set was subjected to three ascertainment schemes: (I) random selection;...

Data from: Contemporary human-altered landscapes and oceanic barriers limit bumble bee gene flow

Shalene Jha
Much of the world's terrestrial landscape is being altered by humans in the form of agriculture, urbanization, and pastoral systems, with major implications for biodiversity. Bumble bees are one of the most effective pollinators in both natural and cultivated landscapes, but are often the first to be extirpated in human-altered habitats. Yet, little is known about the role of natural and human-altered habitats in promoting or limiting bumble bee gene flow. In this study, I...

Data from: Sensory-based niche partitioning in a multiple predator-multiple prey community

Jay J. Falk, Hannah M. Ter Hofstede, Patricia L. Jones, Marjorie M. Dixon, Paul A. Faure, Elisabeth K. V. Kalko & Rachel A. Page
Many predators and parasites eavesdrop on the communication signals of their prey. Eavesdropping is typically studied as dyadic predator–prey species interactions; yet in nature, most predators target multiple prey species and most prey must evade multiple predator species. The impact of predator communities on prey signal evolution is not well understood. Predators could converge in their preferences for conspicuous signal properties, generating competition among predators and natural selection on particular prey signal features. Alternatively, predator...

Data from: Sexual fidelity trade-offs promote regulatory variation in the prairie vole brain

Mariam Okhovat, Alejandro Berrio, Gerard Wallace, Alexander G. Ophir & Steven M. Phelps
Individual variation in social behavior seems ubiquitous, but we know little about how it relates to brain diversity. Among monogamous prairie voles, levels of vasopressin receptor (encoded by the gene avpr1a) in brain regions related to spatial memory predict male space use and sexual fidelity in the field. We find that trade-offs between the benefits of male fidelity and infidelity are reflected in patterns of territorial intrusion, offspring paternity, avpr1a expression, and the evolutionary fitness...

Data from: Gene expression associated with white syndromes in a reef building coral, Acropora hyacinthus

Rachel M. Wright, Galina V. Aglyamova, Eli Meyer & Mikhail V. Matz
Background: Corals are capable of launching diverse immune defenses at the site of direct contact with pathogens, but the molecular mechanisms of this activity and the colony-wide effects of such stressors remain poorly understood. Here we compared gene expression profiles in eight healthy Acropora hyacinthus colonies against eight colonies exhibiting tissue loss commonly associated with white syndromes, all collected from a natural reef environment near Palau. Two types of tissues were sampled from diseased corals:...

Data from: Does plasticity enhance or dampen phenotypic parallelism? A test with three lake-stream stickleback pairs.

Krista B. Oke, Mehvish Bukhari, Renaud Kaeuffer, Gregor Rolshausen, Katja Räsänen, Daniel I. Bolnick, Catherine L. Peichel & Andrew P. Hendry
Parallel (and convergent) phenotypic variation is most often studied in the wild, where it is difficult to disentangle genetic versus environmentally-induced effects. As a result, the potential contributions of phenotypic plasticity to parallelism (and non-parallelism) are rarely evaluated in a formal sense. Phenotypic parallelism could be enhanced by plasticity that causes stronger parallelism across populations in the wild than would be expected from genetic differences alone. Phenotypic parallelism could be dampened if site-specific plasticity induced...

Data from: Controlled measurement and comparative analysis of cellular components in E. coli reveals broad regulatory changes in response to glucose starvation

John R. Houser, Craig Barnhart, Daniel R. Boutz, Sean M. Carrol, Aurko Dasgupta, Joshua K. Michener, Brittany D. Needham, Ophelia Papoulas, Viswanadham Sridhara, Dariya K. Sydykova, Christopher J. Marx, M. Stephen Trent, Jeffery E. Barrick, Edward M. Marcotte, Claus O. Wilke, Jeffrey E. Barrick & Sean M. Carroll
How do bacteria regulate their cellular physiology in response to starvation? Here, we present a detailed characterization of Escherichia coli growth and starvation over a time-course lasting two weeks. We have measured multiple cellular components, including RNA and proteins at deep genomic coverage, as well as lipid modifications and flux through central metabolism. Our study focuses on the physiological response of E. coli in stationary phase as a result of being starved for glucose, not...

Data from: Bacterial cooperation causes systematic errors in pathogen risk assessment due to the failure of the independent action hypothesis

Daniel M. Cornforth, Andrew Matthews, Sam P. Brown & Ben Raymond
The Independent Action Hypothesis (IAH) states that pathogenic individuals (cells, spores, virus particles etc.) behave independently of each other, so that each has an independent probability of causing systemic infection or death. The IAH is not just of basic scientific interest; it forms the basis of our current estimates of infectious disease risk in humans. Despite the important role of the IAH in managing disease interventions for food and water-borne pathogens, experimental support for the...

Data from: Agonistic reciprocity is associated with reduced male reproductive success within haremic social networks

Tessa K. Solomon-Lane, Devaleena S. Pradhan, Madelyne C. Willis & Matthew S. Grober
While individual variation in social behaviour is ubiquitous and causes social groups to differ in structure, how these structural differences affect fitness remains largely unknown. We used social network analysis of replicate bluebanded goby (Lythrypnus dalli) harems to identify the reproductive correlates of social network structure. In stable groups, we quantified agonistic behaviour, reproduction and steroid hormones, which can both affect and respond to social/reproductive cues. We identified distinct, optimal social structures associated with different...

Data from: Metabolic programming mediated by an essential fatty acid alters body composition and survival skills of a marine fish

Lee A. Fuiman & Kestrel O. Perez
Metabolic programming occurs when variations in nutrition during a specific developmental window result in long-term metabolic effects. It has been studied almost exclusively in humans and other mammals but never in an ecological context. Here, we report metabolic programming and its functional consequences in a marine fish, red drum. We demonstrate that maternal provisioning of eggs with an essential fatty acid, docosahexaenoic acid (DHA), varies with DHA content of the maternal diet. When offspring are...

Data from: Sex-specific fitness effects of unpredictable early life conditions are associated with DNA methylation in the avian glucocorticoid receptor

Dustin R. Rubenstein, Hannah Skolnik, Alejandro Berrio, Frances A. Champagne, Steven Phelps & Joseph Solomon
Organisms can adapt to variable environments by using environmental cues to modulate developmental gene expression. In principle, maternal influences can adaptively adjust offspring phenotype when early life and adult environments match, but they may be maladaptive when future environments are not predictable. One of the best-studied ‘maternal effects’ is through modification of the offspring's hypothalamic–pituitary–adrenal (HPA) axis, the neuroendocrine system that controls responses to stress. In addition to the direct transfer of glucocorticoids from mother...

Data from: NDH expression marks major transitions in plant evolution and reveals coordinate intracellular gene loss

Tracey A. Ruhlman, Wang-Jung Chang, Jeremy J. W. Chen, Yao-Ting Huang, Ming-Tsair Chan, Jin Zhang, De-Chih Liao, John C. Blazier, Xiaohua Jin, Ming-Che Shih, Robert K. Jansen & Choun-Sea Lin
Background: Key innovations have facilitated novel niche utilization, such as the movement of the algal predecessors of land plants into terrestrial habitats where drastic fluctuations in light intensity, ultraviolet radiation and water limitation required a number of adaptations. The NDH (NADH dehydrogenase-like) complex of Viridiplantae plastids participates in adapting the photosynthetic response to environmental stress, suggesting its involvement in the transition to terrestrial habitats. Although relatively rare, the loss or pseudogenization of plastid NDH genes...

Data from: Widespread positive but weak assortative mating by diet within stickleback populations

Travis Ingram, Yuexin Jiang, Racine Rangel & Daniel I. Bolnick
Assortative mating – correlation between male and female traits – is common within populations and has the potential to promote genetic diversity and in some cases speciation. Despite its importance, few studies have sought to explain variation in the extent of assortativeness across populations. Here, we measure assortative mating based on an ecologically important trait, diet as inferred from stable isotopes, in 16 unmanipulated lake populations of three-spine stickleback. As predicted, we find a tendency...

Data from: Phylogenetic structural equation modelling reveals no need for an 'origin' of the leaf economics spectrum

Chase M. Mason, Eric W. Goolsby, Devon P. Humphreys & Lisa A. Donovan
The leaf economics spectrum (LES) is a prominent ecophysiological paradigm that describes global variation in leaf physiology across plant ecological strategies using a handful of key traits. Nearly a decade ago, Shipley et al. (2006) used structural equation modelling to explore the causal functional relationships among LES traits that give rise to their strong global covariation. They concluded that an unmeasured trait drives LES covariation, sparking efforts to identify the latent physiological trait underlying the...

Registration Year

  • 2015
    35

Resource Types

  • Dataset
    35

Affiliations

  • The University of Texas at Austin
    35
  • Cornell University
    3
  • Fred Hutchinson Cancer Research Center
    2
  • Columbia University
    2
  • University of Georgia
    2
  • Oregon State University
    2
  • King Abdulaziz University
    2
  • Smithsonian Tropical Research Institute
    2
  • Harvard University
    2
  • University of Kansas
    1