Structure of the plant plastid-encoded RNA polymerase.

Chloroplast genes encoding photosynthesis-associated proteins are predominantly transcribed by the plastid-encoded RNA polymerase (PEP). PEP is a multi-subunit complex composed of plastid-encoded subunits similar to bacterial RNA polymerases (RNAPs) stably bound to a set of nuclear-encoded PEP-associated proteins (PAPs). PAPs are essential to PEP activity and chloroplast biogenesis, but their roles are poorly defined. Here, we present cryoelectron microscopy (cryo-EM) structures of native 21-subunit PEP and a PEP transcription elongation complex from white mustard (Sinapis alba). We identify that PAPs encase the core polymerase, forming extensive interactions that likely promote complex assembly and stability. During elongation, PAPs interact with DNA downstream of the transcription bubble and with the nascent mRNA. The models reveal details of the superoxide dismutase, lysine methyltransferase, thioredoxin, and amino acid ligase enzymes that are subunits of PEP. Collectively, these data provide a foundation for the mechanistic understanding of chloroplast transcription and its role in plant growth and adaptation.

Structural insights into RNA-mediated transcription regulation in bacteria.

RNA can regulate its own synthesis without auxiliary proteins. For example, U-rich RNA sequences signal RNA polymerase (RNAP) to pause transcription and are required for transcript release at intrinsic terminators in all kingdoms of life. In contrast, the regulatory RNA putL suppresses pausing and termination in cis. However, how nascent RNA modulates its own synthesis remains largely unknown. We present cryo-EM reconstructions of RNAP captured during transcription of putL variants or an unrelated sequence at a U-rich pause site. Our results suggest how putL suppresses pausing and promotes its synthesis. We demonstrate that transcribing a U-rich sequence, a ubiquitous trigger of intrinsic termination, promotes widening of the RNAP nucleic-acid-binding channel. Widening destabilizes RNAP interactions with DNA and RNA to facilitate transcript dissociation reminiscent of intrinsic transcription termination. Surprisingly, RNAP remains bound to DNA after transcript release. Our results provide the structural framework to understand RNA-mediated intrinsic transcription termination.

mRNA Deadenylation Is Coupled to Translation Rates by the Differential Activities of Ccr4-Not Nucleases.

Translation and decay of eukaryotic mRNAs is controlled by shortening of the poly(A) tail and release of the poly(A)-binding protein Pab1/PABP. The Ccr4-Not complex contains two exonucleases-Ccr4 and Caf1/Pop2-that mediate mRNA deadenylation. Here, using a fully reconstituted biochemical system with proteins from the fission yeast Schizosaccharomyces pombe, we show that Pab1 interacts with Ccr4-Not, stimulates deadenylation, and differentiates the roles of the nuclease enzymes. Surprisingly, Pab1 release relies on Ccr4 activity. In agreement with this, in vivo experiments in budding yeast show that Ccr4 is a general deadenylase that acts on all mRNAs. In contrast, Caf1 only trims poly(A) not bound by Pab1. As a consequence, Caf1 is a specialized deadenylase required for the selective deadenylation of transcripts with lower rates of translation elongation and reduced Pab1 occupancy. These findings reveal a coupling between the rates of translation and deadenylation that is dependent on Pab1 and Ccr4-Not.

Fundamentally different representations of color and motion revealed by individual differences in perceptual scaling.

The coordinate frames for color and motion are often defined by three dimensions (e.g., responses from the three types of human cone photoreceptors for color and the three dimensions of space for motion). Does this common dimensionality lead to similar perceptual representations? Here we show that the organizational principles for the representation of hue and motion direction are instead profoundly different. We compared observers' judgments of hue and motion direction using functionally equivalent stimulus metrics, behavioral tasks, and computational analyses, and used the pattern of individual differences to decode the underlying representational structure for these features. Hue judgments were assessed using a standard "hue-scaling" task (i.e., judging the proportion of red/green and blue/yellow in each hue). Motion judgments were measured using a "motion-scaling" task (i.e., judging the proportion of left/right and up/down motion in moving dots). Analyses of the interobserver variability in hue scaling revealed multiple independent factors limited to different local regions of color space. This is inconsistent with the influences across a broad range of hues predicted by conventional color-opponent models. In contrast, variations in motion scaling were characterized by more global factors plausibly related to variation in the relative weightings of the cardinal spatial axes. These results suggest that although the coordinate frames for specifying color and motion share a common dimensional structure, the perceptual coding principles for hue and motion direction are distinct. These differences might reflect a distinction between the computational strategies required for the visual analysis of spatial vs. nonspatial attributes of the world.

Genetic Basis and Evolution of Structural Color Polymorphism in an Australian Songbird.

Island organisms often evolve phenotypes divergent from their mainland counterparts, providing a useful system for studying adaptation under differential selection. In the white-winged fairywren (Malurus leucopterus), subspecies on two islands have a black nuptial plumage whereas the subspecies on the Australian mainland has a blue nuptial plumage. The black subspecies have a feather nanostructure that could in principle produce a blue structural color, suggesting a blue ancestor. An earlier study proposed independent evolution of melanism on the islands based on the history of subspecies divergence. However, the genetic basis of melanism and the origin of color differentiation in this group are still unknown. Here, we used whole-genome resequencing to investigate the genetic basis of melanism by comparing the blue and black M. leucopterus subspecies to identify highly divergent genomic regions. We identified a well-known pigmentation gene ASIP and four candidate genes that may contribute to feather nanostructure development. Contrary to the prediction of convergent evolution of island melanism, we detected signatures of a selective sweep in genomic regions containing ASIP and SCUBE2 not in the black subspecies but in the blue subspecies, which possesses many derived SNPs in these regions, suggesting that the mainland subspecies has re-evolved a blue plumage from a black ancestor. This proposed re-evolution was likely driven by a preexisting female preference. Our findings provide new insight into the evolution of plumage coloration in island versus continental populations, and, importantly, we identify candidate genes that likely play roles in the development and evolution of feather structural coloration.

Testosterone Coordinates Gene Expression Across Different Tissues to Produce Carotenoid-Based Red Ornamentation.

Carotenoid pigments underlie most of the red, orange, and yellow visual signals used in mate choice in vertebrates. However, many of the underlying processes surrounding the production of carotenoid-based traits remain unclear due to the complex nature of carotenoid uptake, metabolism, and deposition across tissues. Here, we leverage the ability to experimentally induce the production of a carotenoid-based red plumage patch in the red-backed fairywren (Malurus melanocephalus), a songbird in which red plumage is an important male sexual signal. We experimentally elevated testosterone in unornamented males lacking red plumage to induce the production of ornamentation and compared gene expression in both the liver and feather follicles between unornamented control males, testosterone-implanted males, and naturally ornamented males. We show that testosterone upregulates the expression of CYP2J19, a gene known to be involved in ketocarotenoid metabolism, and a putative carotenoid processing gene (ELOVL6) in the liver, and also regulates the expression of putative carotenoid transporter genes in red feather follicles on the back, including ABCG1. In black feathers, carotenoid-related genes are downregulated and melanin genes upregulated, but we find that carotenoids are still present in the feathers. This may be due to the activity of the carotenoid-cleaving enzyme BCO2 in black feathers. Our study provides a first working model of a pathway for carotenoid-based trait production in free-living birds, implicates testosterone as a key regulator of carotenoid-associated gene expression, and suggests hormones may coordinate the many processes that underlie the production of these traits across multiple tissues.

Nestling Begging Calls Resemble Maternal Vocal Signatures When Mothers Call Slowly to Embryos.

AbstractVocal production learning (the capacity to learn to produce vocalizations) is a multidimensional trait that involves different learning mechanisms during different temporal and socioecological contexts. Key outstanding questions are whether vocal production learning begins during the embryonic stage and whether mothers play an active role in this through pupil-directed vocalization behaviors. We examined variation in vocal copy similarity (an indicator of learning) in eight species from the songbird family Maluridae, using comparative and experimental approaches. We found that (1) incubating females from all species vocalized inside the nest and produced call types including a signature "B element" that was structurally similar to their nestlings' begging call; (2) in a prenatal playback experiment using superb fairy wrens (Malurus cyaneus), embryos showed a stronger heart rate response to playbacks of the B element than to another call element (A); and (3) mothers that produced slower calls had offspring with greater similarity between their begging call and the mother's B element vocalization. We conclude that malurid mothers display behaviors concordant with pupil-directed vocalizations and may actively influence their offspring's early life through sound learning shaped by maternal call tempo.

Climate-mediated population dynamics of a migratory songbird differ between the trailing edge and range core.

Understanding the demographic drivers of range contractions is important for predicting species' responses to climate change; however, few studies have examined the effects of climate change on survival and recruitment across species' ranges. We show that climate change can drive trailing edge range contractions through the effects on apparent survival, and potentially recruitment, in a migratory songbird. We assessed the demographic drivers of trailing edge range contractions using a long-term demography dataset for the black-throated blue warbler (Setophaga caerulescens) collected across elevational climate gradients at the trailing edge and core of the breeding range. We used a Bayesian hierarchical model to estimate the effect of climate change on apparent survival and recruitment and to forecast population viability at study plots through 2040. The trailing edge population at the low-elevation plot became locally extinct by 2017. The local population at the mid-elevation plot at the trailing edge gradually declined and is predicted to become extirpated by 2040. Population declines were associated with warming temperatures at the mid-elevation plot, although results were more equivocal at the low-elevation plot where we had fewer years of data. Population density was stable or increasing at the range core, although warming temperatures are predicted to cause population declines by 2040 at the low-elevation plot. This result suggests that even populations within the geographic core of the range are vulnerable to climate change. The demographic drivers of local population declines varied between study plots, but warming temperatures were frequently associated with declining rates of population growth and apparent survival. Declining apparent survival in our study system is likely to be associated with increased adult emigration away from poor-quality habitats. Our results suggest that demographic responses to warming temperatures are complex and dependent on local conditions and geographic range position, but spatial variation in population declines is consistent with the climate-mediated range shift hypothesis. Local populations of black-throated blue warblers near the warm-edge range boundary at low latitudes and low elevations are likely to be the most vulnerable to climate change, potentially leading to local extirpation and range contractions.

Low-coverage whole genome sequencing for highly accurate population assignment: Mapping migratory connectivity in the American Redstart (Setophaga ruticilla).

Understanding the geographic linkages among populations across the annual cycle is an essential component for understanding the ecology and evolution of migratory species and for facilitating their effective conservation. While genetic markers have been widely applied to describe migratory connections, the rapid development of new sequencing methods, such as low-coverage whole genome sequencing (lcWGS), provides new opportunities for improved estimates of migratory connectivity. Here, we use lcWGS to identify fine-scale population structure in a widespread songbird, the American Redstart (Setophaga ruticilla), and accurately assign individuals to genetically distinct breeding populations. Assignment of individuals from the nonbreeding range reveals population-specific patterns of varying migratory connectivity. By combining migratory connectivity results with demographic analysis of population abundance and trends, we consider full annual cycle conservation strategies for preserving numbers of individuals and genetic diversity. Notably, we highlight the importance of the Northern Temperate-Greater Antilles migratory population as containing the largest proportion of individuals in the species. Finally, we highlight valuable considerations for other population assignment studies aimed at using lcWGS. Our results have broad implications for improving our understanding of the ecology and evolution of migratory species through conservation genomics approaches.

Systems biology as a framework to understand the physiological and endocrine bases of behavior and its evolution-From concepts to a case study in birds.

Organismal behavior, with its tremendous complexity and diversity, is generated by numerous physiological systems acting in coordination. Understanding how these systems evolve to support differences in behavior within and among species is a longstanding goal in biology that has captured the imagination of researchers who work on a multitude of taxa, including humans. Of particular importance are the physiological determinants of behavioral evolution, which are sometimes overlooked because we lack a robust conceptual framework to study mechanisms underlying adaptation and diversification of behavior. Here, we discuss a framework for such an analysis that applies a "systems view" to our understanding of behavioral control. This approach involves linking separate models that consider behavior and physiology as their own networks into a singular vertically integrated behavioral control system. In doing so, hormones commonly stand out as the links, or edges, among nodes within this system. To ground our discussion, we focus on studies of manakins (Pipridae), a family of Neotropical birds. These species have numerous physiological and endocrine specializations that support their elaborate reproductive displays. As a result, manakins provide a useful example to help imagine and visualize the way systems concepts can inform our appreciation of behavioral evolution. In particular, manakins help clarify how connectedness among physiological systems-which is maintained through endocrine signaling-potentiate and/or constrain the evolution of complex behavior to yield behavioral differences across taxa. Ultimately, we hope this review will continue to stimulate thought, discussion, and the emergence of research focused on integrated phenotypes in behavioral ecology and endocrinology.

Automatic, Early Color-Specific Neural Responses to Object Color Knowledge.

Some familiar objects are associated with specific colors, e.g., rubber ducks with yellow. Whether and at what stage neural responses occur to these color associations remain open questions. We recorded frequency-tagged electroencephalogram (EEG) responses to periodic presentations of yellow-associated objects, shown among sequences of non-periodic blue-, red-, and green-associated objects. Both color and grayscale versions of the objects elicited yellow-specific responses, indicating an automatic activation of color knowledge from object shape. Follow-up experiments replicated these effects with green-specific responses, and demonstrated modulated responses for incongruent color/object associations. Importantly, the onset of color-specific responses was as early to grayscale as actually colored stimuli (before 100 ms), the latter additionally eliciting a conventional later response (approximately 140-230 ms) to actual stimulus color. This suggests that the neural representation of familiar objects includes both diagnostic shape and color properties, such that shape can elicit associated color-specific responses before actual color-specific responses occur.

Gaining the system: limits to compensating color deficiencies through post-receptoral gain changes.

Color percepts of anomalous trichromats are often more similar to normal trichromats than predicted from their receptor spectral sensitivities, suggesting that post-receptoral mechanisms can compensate for chromatic losses. The basis for these adjustments and the extent to which they could discount the deficiency are poorly understood. We modeled the patterns of compensation that might result from increasing the gains in post-receptoral neurons to offset their weakened inputs. Individual neurons and the population responses jointly encode luminance and chromatic signals. As a result, they cannot independently adjust for a change in the chromatic inputs, predicting only partial recovery of the chromatic responses and increased responses to achromatic contrast. These analyses constrain the potential sites and mechanisms of compensation for a color loss and characterize the utility and limits of neural gain changes for calibrating color vision.

Using equiluminance settings to estimate the cardinal chromatic directions for individuals.

Color information is processed by the retina and lateral geniculate along principal dimensions known as the cardinal directions of color space. Normal differences in spectral sensitivity can impact the stimulus directions that isolate these axes for individual observers and can arise from variation in lens and macular pigment density, photopigment opsins, photoreceptor optical density, and relative cone numbers. Some of these factors that influence the chromatic cardinal axes also impact luminance sensitivity. We modeled and empirically tested how well tilts on the individual's equiluminant plane are correlated with rotations in the directions of their cardinal chromatic axes. Our results show that, especially for the SvsLM axis, the chromatic axes can be partially predicted by luminance settings, providing a potential procedure for efficiently characterizing the cardinal chromatic axes for observers.

Poster Session: Achromatic biases in noise images.

In a previous study, Winkler et al. (Current Bio 2015) examined the effects of luminance on the perceived color categories selected for uniform square patches. When the square was equiluminant with the background, the patch appeared colored as soon as it was detected, while for increments or decrements, the range of chromaticities that were classified as achromatic was expanded and more strongly along bluish axes. Here we extended these results to examine the color appearance of spatially varying patterns, which contain a wide range of luminance levels. The images were 1/f luminance noise and were briefly alternated with a gray background with the same mean luminance. The noise was shown on each trial with a uniform chromaticity, which was varied across trials over a grid of values spanning the LvsM and SvsLM cone-opponent axes. Observers categorized each noise image as gray or one of the four unique (RGBY) or binary (RB,BG,GY,YR) hues. The perceived achromatic gamut for the noise again tended to vary along bluish-yellowish directions, but was markedly broader compared to the uniform patches. The broadening of the gray category may partly reflect attributions of some of the color to the illuminant, a tendency which may be stronger in the spatially variegated patterns.

Poster Session: A direct measure of adaptation and visual salience.

One hypothesized function of adaptation is to increase the salience of novel targets by discounting the properties of the ambient environment. Previous studies have suggested this by finding faster search times for novel targets when searching on backgrounds observers are currently adapted to. However, this provides only an indirect measure of salience. Here, we developed a more direct measure of the impact of adaptation on feature salience. Backgrounds were oriented 1/f noise images with power confined within 15 deg of horizontal or vertical. Targets were 5 c/deg Gabor patches centered on the 8 deg backgrounds. Observers simultaneously adapted to the horizontal or vertical backgrounds shown on the left or right of fixation. A 250ms test probe then showed the Gabor patch on the same background (horizontal or vertical) on both sides. The target orientation was adjusted on one side until it appeared as conspicuous as a fixed target on the other side. Settings were made for fixed targets ranging from 10 to 45 deg from the backgrounds. For most conditions/observers, the salience matches required a smaller orientation offset on the same- vs. different-adapt background. These results support a functional role of adaptation in highlighting novelty by potentially "unmasking" the target from its background, and emphasize the importance of considering adaptation aftereffects not only for isolated targets but within the stimulus contexts they are embedded in.

Intersexual social dominance mimicry drives female hummingbird polymorphism.

Female-limited polymorphisms, where females have multiple forms but males have only one, have been described in a variety of animals, yet are difficult to explain because selection typically is expected to decrease rather than maintain diversity. In the white-necked jacobin (Florisuga mellivora), all males and approximately 20% of females express an ornamented plumage type (androchromic), while other females are non-ornamented (heterochromic). Androchrome females benefit from reduced social harassment, but it remains unclear why both morphs persist. Female morphs may represent balanced alternative behavioural strategies, but an alternative hypothesis is that androchrome females are mimicking males. Here, we test a critical prediction of these hypotheses by measuring morphological, physiological and behavioural traits that relate to resource-holding potential (RHP), or competitive ability. In all these traits, we find little difference between female types, but higher RHP in males. These results, together with previous findings in this species, indicate that androchrome females increase access to food resources through mimicry of more aggressive males. Importantly, the mimicry hypothesis provides a clear theoretical pathway for polymorphism maintenance through frequency-dependent selection. Social dominance mimicry, long suspected to operate between species, can therefore also operate within species, leading to polymorphism and perhaps similarities between sexes more generally.

Adapting to an enhanced color gamut - implications for color vision and color deficiencies.

One strategy for aiding color deficiencies is to use three narrow passbands to filter the light spectrum to increase the saturation of colors. This filtering is analogous to the narrow emission bands used in wide gamut lighting or displays. We examined how perception adapts to the greater color gamut area produced by such devices, testing color-normal observers and simulated environments. Narrowband spectra increased chromatic contrasts but also increased contrast adaptation, partially offsetting the perceived contrast enhancements. Such adaptation adjustments are important for understanding the perceptual consequences of exposure to naturally or artificially enhanced color gamut areas for both color-deficient and color-normal observers.

Digital Extended Specimens: Enabling an Extensible Network of Biodiversity Data Records as Integrated Digital Objects on the Internet.

The early twenty-first century has witnessed massive expansions in availability and accessibility of digital data in virtually all domains of the biodiversity sciences. Led by an array of asynchronous digitization activities spanning ecological, environmental, climatological, and biological collections data, these initiatives have resulted in a plethora of mostly disconnected and siloed data, leaving to researchers the tedious and time-consuming manual task of finding and connecting them in usable ways, integrating them into coherent data sets, and making them interoperable. The focus to date has been on elevating analog and physical records to digital replicas in local databases prior to elevating them to ever-growing aggregations of essentially disconnected discipline-specific information. In the present article, we propose a new interconnected network of digital objects on the Internet-the Digital Extended Specimen (DES) network-that transcends existing aggregator technology, augments the DES with third-party data through machine algorithms, and provides a platform for more efficient research and robust interdisciplinary discovery.

Assessing the potential for demographic restoration and assisted evolution to build climate resilience in coral reefs.

Interest is growing in developing conservation strategies to restore and maintain coral reef ecosystems in the face of mounting anthropogenic stressors, particularly climate warming and associated mass bleaching events. One such approach is to propagate coral colonies ex situ and transplant them to degraded reef areas to augment habitat for reef-dependent fauna, prevent colonization from spatial competitors, and enhance coral reproductive output. In addition to such "demographic restoration" efforts, manipulating the thermal tolerance of outplanted colonies through assisted relocation, selective breeding, or genetic engineering is being considered for enhancing rates of evolutionary adaptation to warming. Although research into such "assisted evolution" strategies has been growing, their expected performance remains unclear. We evaluated the potential outcomes of demographic restoration and assisted evolution in climate change scenarios using an eco-evolutionary simulation model. We found that supplementing reefs with pre-existing genotypes (demographic restoration) offers little climate resilience benefits unless input levels are large and maintained for centuries. Supplementation with thermally resistant colonies was successful at improving coral cover at lower input levels, but only if maintained for at least a century. Overall, we found that, although demographic restoration and assisted evolution have the potential to improve long-term coral cover, both approaches had a limited impact in preventing severe declines under climate change scenarios. Conversely, with sufficient natural genetic variance and time, corals could readily adapt to warming temperatures, suggesting that restoration approaches focused on building genetic variance may outperform those based solely on introducing heat-tolerant genotypes.

Grenz ray therapy in disseminated superficial actinic porokeratosis: A case series of 17 patients.

The treatments available for disseminated superficial actinic porokeratosis (DSAP) have been limited and have variable efficacy. We report the largest case series to date of the use of Grenz ray therapy in 17 patients with DSAP. There was at least 50% improvement in DSAP lesions in all cases. Erythema, itching and burning were common side effects of Grenz ray therapy. We believe that Grenz ray therapy may be an effective treatment option for patients with DSAP.