The little skate genome and the evolutionary emergence of wing-like fins

Skates are cartilaginous fish whose body plan features enlarged wing-like pectoral fins, enabling them to thrive in benthic environments1,2. However, the molecular underpinnings of this unique trait remain unclear. Here we investigate the origin of this phenotypic innovation by developing the little skate Leucoraja erinacea as a genomically enabled model. Analysis of a high-quality chromosome-scale genome sequence for the little skate shows that it preserves many ancestral jawed vertebrate features compared with other sequenced genomes, including numerous ancient microchromosomes. Combining genome comparisons with extensive regulatory datasets in developing fins—including gene expression, chromatin occupancy and three-dimensional conformation—we find skate-specific genomic rearrangements that alter the three-dimensional regulatory landscape of genes that are involved in the planar cell polarity pathway. Functional inhibition of planar cell polarity signalling resulted in a reduction in anterior fin size, confirming that this pathway is a major contributor to batoid fin morphology. We also identified a fin-specific enhancer that interacts with several hoxa genes, consistent with the redeployment of hox gene expression in anterior pectoral fins, and confirmed its potential to activate transcription in the anterior fin using zebrafish reporter assays. Our findings underscore the central role of genome reorganization and regulatory variation in the evolution of phenotypes, shedding light on the molecular origin of an enigmatic trait

The little skate genome and the evolutionary emergence of wing-like fin appendages

Skates are cartilaginous fish whose novel body plan features remarkably enlarged wing-like pectoral fins that allow them to thrive in benthic environments. The molecular underpinnings of this unique trait, however, remain elusive. Here we investigate the origin of this phenotypic innovation by developing the little skate Leucoraja erinacea as a genomically enabled model. Analysis of a high-quality chromosome-scale genome sequence for the little skate shows that it preserves many ancestral jawed vertebrate features compared with other sequenced genomes, including numerous ancient microchromosomes. Combining genome comparisons with extensive regulatory datasets in developing fins (gene expression, chromatin occupancy and three-dimensional (3D) conformation) we find skate-specific genomic rearrangements that alter the 3D regulatory landscape of genes involved in the planar cell polarity (PCP) pathway. Functional inhibition of PCP signaling resulted in marked reduction of anterior fin size, confirming this pathway as a major contributor of batoid fin morphology. We also identified a fin-specific enhancer that interacts with 3' HOX genes, consistent with the redeployment of Hox gene expression in anterior pectoral fins, and confirmed the potential of this element to activate transcription in the anterior fin using zebrafish reporter assays. Our findings underscore the central role of genome reorganizations and regulatory variation in the evolution of phenotypes, shedding light on the molecular origin of an enigmatic trait

Building a topographical model for the Roman town of Ammaia

In the framework of the projects: FP7 Marie Curie/People IAPP 2008, Radio-Past GA 230679. FCOMP-01-0124-FEDER-010492Peer reviewe

Dairy products, surrogate markers, and cardiovascular disease; a sex-specific analysis from the ATTICA prospective study

Background and aims: Dairy products are a very diverse food group with multiple effects on the cardiac health of men and women. The aim of this work was to evaluate the sex-specific association between dairy products (total and subtypes) and 10-year first fatal/nonfatal cardiovascular disease (CVD) incidence. Methods and results: In 2001–2002, n = 1514 men and n = 1528 women (>18 years old) from greater Athens area, Greece, were enrolled. Dietary assessment was based on a validated semi-quantitative food frequency questionnaire. Dairy product consumption was examined in relation to 10-year CVD incidence. Follow-up (2011–2012) was achieved in n = 2020 participants (n = 317 CVD cases). Ranking from lowest (<1 serving/day) to highest (>2 servings/day) total dairy intake, CVD incidence in men was 17.8%, 15.0%, and 10.9% (p = 0.41), while in women it was 14%, 6.0%, and 5.7% (p = 0.02). Multiadjusted analysis revealed that total dairy intake protected against CVD only in women [Hazard Ratio (HR) = 0.48 and 95% Confidence Interval (95% CI) (0.23, 0.90)], irrespective of the fat content. Further analysis revealed that only fermented products (yogurt and cheese), protected against CVD. For per 200 g/day yogurt consumption, CVD risk was 20%–30% lower with this claim being more evident in women, while for per 30 g/day cheese intake, about 5% lower risk was observed particularly in men. As for butter, nonsignificant associations were highlighted. These associations were mainly retained in the case of hepatic steatosis, insulin resistance, and systemic inflammation. Conclusions: This work provides incentives for researchers to elucidate the diversity of ingredients and mechanisms through which dairy products exert their effect on cardiac health separately for men and women. © 2020 The Italian Diabetes Society, the Italian Society for the Study of Atherosclerosis, the Italian Society of Human Nutrition and the Department of Clinical Medicine and Surgery, Federico II Universit

An Experiment in Using Visual Attention Metrics to Think About Experience and Design Choices in Past Places

The influence of the visual properties of a built space or landscape on the behaviors of people within them and the manipulation of these visual properties to cue or constrain behaviors are subjects of long-standing archaeological interest. Advances in cognitive neurosciences and a suite of improved computational modeling tools, combined with the proliferation of detailed 3D models of archaeological complexes and landscapes, offer an opportunity for new approaches to these topics based on models of low-level perceptual cues and visual attention. The approach described here takes aim at the question of where people will look, rather than simply what is visible, with the goal of investigating the intentions of designers of spaces and visual aspects of the experience of a place. In simple terms, our approach involves placing detailed 3D models of built spaces or landscapes into a digital environment. An individual then virtually walks through the space and what is visible at each moment is recorded in the form of a video stream, which may be broken down into a sequence of scenes. This set of scenes is then analyzed using software that calculates and maps the visual saliency of each scene and the path of focuses of attention (FOAs) over time. This set of saliency maps, raw images, and FOA paths provide the basis for further interpretation. This paper presents an initial experiment to illustrate the approach, carried out in the eastern passage at Knowth, one of the main mounds in the Brú na Bóinne in Ireland

Exploring Transformations in Caribbean Indigenous Social Networks through Visibility Studies: the Case of Late Pre-Colonial Landscapes in East-Guadeloupe (French West Indies)

This paper presents a study of the visual properties of natural and Amerindian cultural landscapes in late pre-colonial East-Guadeloupe and of how these visual properties affected social interactions. Through a review of descriptive and formal visibility studies in Caribbean archaeology, it reveals that the ability of visual properties to affect past human behaviour is frequently evoked but the more complex of these hypotheses are rarely studied formally. To explore such complex hypotheses, the current study applies a range of techniques: total viewsheds, cumulative viewsheds, visual neighbourhood configurations and visibility networks. Experiments were performed to explore the control of seascapes, the functioning of hypothetical smoke signalling networks, the correlation of these visual properties with stylistic similarities of material culture found at sites and the change of visual properties over time. The results of these experiments suggest that only few sites in Eastern Guadeloupe are located in areas that are particularly suitable to visually control possible sea routes for short- and long-distance exchange; that visual control over sea areas was not a factor of importance for the existence of micro-style areas; that during the early phase of the Late Ceramic Age networks per landmass are connected and dense and that they incorporate all sites, a structure that would allow hypothetical smoke signalling networks; and that the visual properties of locations of the late sites Morne Souffleur and Morne Cybèle-1 were not ideal for defensive purposes. These results led us to propose a multi-scalar hypothesis for how lines of sight between settlements in the Lesser Antilles could have structured past human behaviour: short-distance visibility networks represent the structuring of navigation and communication within landmasses, whereas the landmasses themselves served as focal points for regional navigation and interaction. We conclude by emphasising that since our archaeological theories about visual properties usually take a multi-scalar landscape perspective, there is a need for this perspective to be reflected in our formal visibility methods as is made possible by the methods used in this paper.Digital ArchaeologyArchaeology of the America

Dynamic 3D chromatin architecture contributes to enhancer specificity and limb morphogenesis

The regulatory specificity of enhancers and their interaction with gene promoters is thought to be controlled by their sequence and the binding of transcription factors. By studying Pitx1, a regulator of hindlimb development, we show that dynamic changes in chromatin conformation can restrict the activity of enhancers. Inconsistent with its hindlimb-restricted expression, Pitx1 is controlled by an enhancer (Pen) that shows activity in forelimbs and hindlimbs. By Capture Hi-C and three-dimensional modeling of the locus, we demonstrate that forelimbs and hindlimbs have fundamentally different chromatin configurations, whereby Pen and Pitx1 interact in hindlimbs and are physically separated in forelimbs. Structural variants can convert the inactive into the active conformation, thereby inducing Pitx1 misexpression in forelimbs, causing partial arm-to-leg transformation in mice and humans. Thus, tissue-specific three-dimensional chromatin conformation can contribute to enhancer activity and specificity in vivo and its disturbance can result in gene misexpression and disease