Out of Florida: mtDNA reveals patterns of migration and Pleistocene range expansion of the Green Anole lizard (Anolis carolinensis)

Anolis carolinensis is an emerging model species and the sole member of its genus native to the United States. Considerable morphological and physiological variation has been described in the species, and the recent sequencing of its genome makes it an attractive system for studies of genome variation. To inform future studies of molecular and phenotypic variation within A. carolinensis, a rigorous account of intraspecific population structure and relatedness is needed. Here, we present the most extensive phylogeographic study of this species to date. Phylogenetic analyses of mitochondrial DNA sequence data support the previous hypothesis of a western Cuban origin of the species. We found five well-supported, geographically distinct mitochondrial haplotype clades throughout the southeastern United States. Most Florida populations fall into one of three divergent clades, whereas the vast majority of populations outside Florida belong to a single, shallowly diverged clade. Genetic boundaries do not correspond to major rivers, but may reflect effects of Pleistocene glaciation events and the Appalachian Mountains on migration and expansion of the species. Phylogeographic signal should be examined using nuclear loci to complement these findings.Organismic and Evolutionary Biolog

Real-Time Visualization and Quantitation of Vascular Permeability In Vivo: Implications for Drug Delivery

The leaky, heterogeneous vasculature of human tumors prevents the even distribution of systemic drugs within cancer tissues. However, techniques for studying vascular delivery systems in vivo often require complex mammalian models and time-consuming, surgical protocols. The developing chicken embryo is a well-established model for human cancer that is easily accessible for tumor imaging. To assess this model for the in vivo analysis of tumor permeability, human tumors were grown on the chorioallantoic membrane (CAM), a thin vascular membrane which overlays the growing chick embryo. The real-time movement of small fluorescent dextrans through the tumor vasculature and surrounding tissues were used to measure vascular leak within tumor xenografts. Dextran extravasation within tumor sites was selectively enhanced an interleukin-2 (IL-2) peptide fragment or vascular endothelial growth factor (VEGF). VEGF treatment increased vascular leak in the tumor core relative to surrounding normal tissue and increased doxorubicin uptake in human tumor xenografts. This new system easily visualizes vascular permeability changes in vivo and suggests that vascular permeability may be manipulated to improve chemotherapeutic targeting to tumors

AgBioData consortium recommendations for sustainable genomics and genetics databases for agriculture

The future of agricultural research depends on data. The sheer volume of agricultural biological data being produced today makes excellent data management essential. Governmental agencies, publishers and science funders require data management plans for publicly funded research. Furthermore, the value of data increases exponentially when they are properly stored, described, integrated and shared, so that they can be easily utilized in future analyses. AgBioData (https://www.agbiodata.org) is a consortium of people working at agricultural biological databases, data archives and knowledgbases who strive to identify common issues in database development, curation and management, with the goal of creating database products that are more Findable, Accessible, Interoperable and Reusable. We strive to promote authentic, detailed, accurate and explicit communication between all parties involved in scientific data. As a step toward this goal, we present the current state of biocuration, ontologies, metadata and persistence, database platforms, programmatic (machine) access to data, communication and sustainability with regard to data curation. Each section describes challenges and opportunities for these topics, along with recommendations and best practices

AgBioData consortium recommendations for sustainable genomics and genetics databases for agriculture

The future of agricultural research depends on data. The sheer volume of agricultural biological data being produced today makes excellent data management essential. Governmental agencies, publishers and science funders require datamanagement plans for publicly funded research. Furthermore, the value of data increases exponentially when they are properly stored, described, integrated and shared, so that they can be easily utilized in future analyses. AgBioData (https://www.agbiodata.org) is a consortium of people working at agricultural biological databases, data archives and knowledgbases who strive to identify common issues in database development, curation and management, with the goal of creating database products that are more Findable, Accessible, Interoperable and Reusable. We strive to promote authentic, detailed, accurate and explicit communication between all parties involved in scientific data. As a step toward this goal, we present the current state of biocuration, ontologies, metadata and persistence, database platforms, programmatic (machine) access to data, communication and sustainability with regard to data curation. Each section describes challenges and opportunities for these topics, along with recommendations and best practices

Annual Research Review: Sleep problems in childhood psychiatric disorders – a review of the latest science

Background Hippocrates flagged the value of sleep for good health. Nonetheless, historically, researchers with an interest in developmental psychopathology have largely ignored a possible role for atypical sleep. Recently, however, there has been a surge of interest in this area, perhaps reflecting increased evidence that disturbed or insufficient sleep can result in poor functioning in numerous domains. This review outlines what is known about sleep in the psychiatric diagnoses most relevant to children and for which associations with sleep are beginning to be understood. While based on a comprehensive survey of the literature, the focus of the current review is on the latest science (largely from 2010). There is a description of both concurrent and longitudinal links as well as possible mechanisms underlying associations. Preliminary treatment research is also considered which suggests that treating sleep difficulties may result in improvements in behavioural areas beyond sleep quality. Findings To maximise progress in this field, there now needs to be: (a) greater attention to the assessment of sleep in children; (b) sleep research on a wider range of psychiatric disorders; (c) a greater focus on and examination of mechanisms underlying associations; (d) a clearer consideration ofdevelopmental questions and (e) large-scale well-designed treatment studies. Conclusions While sleep problems may sometimes be missed by parents and healthcare providers; hence constituting a hidden risk for other psychopathologies – knowing about these difficulties creates unique opportunities. The current excitement in this field from experts in diverse areas including developmental psychology, clinical psychology, genetics and neuropsychology should make these opportunities a reality

Phylogeographic History and Temperature-Mediated Evolution of the Green Anole, Anolis Carolinensis

Temperature plays an important role in shaping the form and function of every species. Ectothermic organisms are particularly sensitive to fluctuations in their thermal environment. Their inability to produce appreciable amounts of heat through physiological mechanisms makes them particularly vulnerable to thermal shifts, and ideal for the study of temperature-mediated evolution. The central goal of this dissertation is to understand how temperature shapes the evolutionary history of terrestrial ectotherms during the colonization of novel environments. Towards this aim, I focus on a single species of lizard, the North American green anole, Anolis carolinensis. In the first chapter of my dissertation I trace the phylogeographic history of A. carolinensis in order to identify the geographic distribution of major genetic lineages within the species and its Cuban relatives, date times of divergence between these lineages, and identify geographic barriers to dispersal. In the second chapter, I use an integrated approach to identify aspects of the environment that may have influenced evolutionary adaptation within the species. I combine geo-referenced climate data, environmental niche modeling, thermal physiology, common garden experiments and genomic techniques to understand phenotypic and genomic response of this historically subtropical Cuban lizard to the more temperate regions of the American Southeast. Finally, in the third chapter I use experimental temperature manipulations and physiological testing to explore the roles of phenotypic plasticity and local adaptation in shaping latitudinal variation in thermal tolerance and identify potential systemic mechanisms involved. As a result, I have identified a Miocene origin of the initial over-water dispersal event leading to the establishment of the green anole in peninsular Florida, followed by a rapid Pleistocene range expansion of the species northward into higher latitudes. Range expansion on the mainland has led to thermal niche expansion, mediated by a combination of local adaptation of cold tolerance and genetic isolation by environment between populations from different thermal habitats. Phenotypic plasticity and canalized differentiation both shape variation in cold tolerance across latitude and energy conservation via metabolic suppression under acute and chronic cold onset may help to extend the limits of cold tolerance in this species at its northernmost latitudes.Biology, Organismic and Evolutionar

Next-generation sequencing and the expanding domain of phylogeography

Phylogeography is experiencing a revolution brought on by next generation sequencing methods. A historical survey of the phylogeographic literature suggests that phylogeography typically incorporates new questions, expanding on its classical domain, when new technologies offer novel or increased numbers of molecular markers. A variety of methods for subsampling genomic variation, including Restriction site associated DNA sequencing (Rad-seq) and other next generation approaches, are proving exceptionally useful in helping define major phylogeographic lineages within species as well as details of historical demography. Next generation methods are also blurring the edges of phylogeography and related fields such as association mapping of loci under selection, and the emerging paradigm is one of simultaneously inferring both population history across geography and genomic targets of selection. However, recent examples, including some from our lab on Anolis lizards and songbirds, suggest that genome subsampling methods, while extremely powerful for the classical goals of phylogeography, may fail to allow phylogeography to fully achieve the goals of this new, expanded domain. Specifically, if genome-wide linkage disequilibrium is low, as is the case in many species with large population sizes, most genome subsampling methods will not sample densely enough to detect selected variants, or variants closely linked to them. We suggest that whole-genome resequencing methods will be essential for allowing phylogeographers to robustly identify loci involved in phenotypic divergence and speciation, while at the same time allowing free choice of molecular markers and further resolution of the demographic history of species.Organismic and Evolutionary Biolog