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Abstract Background Cancer is the leading cause of disease-related mortality in children. Causes of leukemia, the most common form, are largely unknown. Growing evidence points to an origin in-utero, when global redistribution of DNA methylation occurs driving tissue differentiation. Methods Epigenome-wide DNA methylation was profiled in surrogate (blood) and target (bone marrow) tissues at birth, diagnosis, remission and relapse of pediatric pre-B acute lymphoblastic leukemia (pre-B ALL) patients. Double-blinded analyses was performed between prospective cohorts extending from birth to diagnosis and retrospective studies backtracking from clinical disease to birth. Validation was carried out using independent technologies and populations. Results The imprinted and immuno-modulating VTRNA2-1 was hypermethylated (FDR

Natural history museums are vital repositories of specimens, samples and data that inform about the natural world; this Formal Comment revisits a Perspective that advocated for the adoption of compassionate collection practices, querying whether it will ever be possible to completely do away with whole animal specimen collection.

The Indo-Australian Archipelago (IAA) is a geologically dynamic area of high biotic endemism that spans the continental shelves of Sunda and Sahul and intervening oceanic islands. We provide a comprehensive quantitative assessment of how bird communities are structured across the IAA using beta diversity indices. We focus on three key questions. Are the islands of Wallacea a biogeographically cohesive unit or a more heterogeneous transition zone? Is the rich biota of New Guinea and the East Melanesian islands most closely linked to that of Sunda, Sahul or Wallacea? What are the geographic and environmental correlates of biotic structuring across the region and how does this compare with determinants of plant diversity? We measure the dissimilarity of bird species composition between eleven major areas within the IAA using a new compilation of distribution data and calculate taxonomic beta diversity at species, genera, and family levels. To compare with recent analyses of plants, we analysed potential correlates of turnover, focusing on geographic proximity, sea barriers, land area, and climatic variation. We also used connectivity analyses to estimate the minimum number of connection events needed to explain the current distribution of shared taxa. We found that islands recently connected by land have lower beta diversity than oceanic islands. Additionally, avifaunas on the islands of Wallacea have little biotic cohesion, reflecting their complex geological history. The avifaunas of New Guinea and the Eastern Melanesian islands are very distinctive. Where New Guinea birds are most similar to Australia, East Melanesian birds are more similar to either Sahul or Wallacea, depending on taxonomic level. Isolation through space and time had the strongest influence on avifaunal turnover at all taxonomic scales, in contrast to plants for which climatic variation was the strongest predictor. Further analyses incorporating phylogeny, biome, trait, and biotic interaction data are needed to investigate the processes that have caused biotic turnover across this fascinating biogeographic region.

It has been proposed that children with acute lymphoblastic leukemia (ALL) are born with a dysregulated immune function that together with postnatal environmental exposures causes childhood ALL. Despite its importance for the understanding of ALL etiology, this hypothesis has been inadequately explored. In a population-based case-control study, we measured the concentrations of 10 cytokines and other inflammatory markers on neonatal dried blood spots from 178 children who at ages 1 to 9 years were diagnosed with B-cell precursor ALL and 178 matched controls. Through linkage with Danish nationwide registers, we also assessed whether neonatal inflammatory markers were associated with previously demonstrated risk factors for childhood ALL. Children who developed B-cell precursor ALL had significantly lower neonatal concentrations of IL8, soluble IL6 receptor (sIL6R) α, TGFβ1, monocyte chemotactic protein (MCP)-1, and C-reactive protein (CRP) and higher concentrations of IL6, IL17, and IL18 compared with matched controls. Concentrations of IL10 were below the detection level for both patients and controls. Birth order (IL18 and CRP), gestational age (sIL6Rα, TGFβ1, and CRP), and sex (sIL6Rα, IL8, and CRP), but not maternal age, infections during pregnancy, birth weight nor mode of delivery were significantly associated with the neonatal concentrations of inflammatory markers. Our findings support the hypothesis that children who later develop B-cell precursor ALL are born with a dysregulated immune function.Significance: Children who develop acute lymphoblastic leukemia are immunologically distinct at birth and could potentially react abnormally to infections in early childhood. Cancer Res; 78(18); 5458-63. ©2018 AACR.

AIM: Rump plumage coloration of the Eastern Yellow Robin (Eopsaltria australis), a widespread Australian songbird, varies from bright yellow in the tropical north to oliveâgreen in the temperate south. Here, we test whether colour variation: (1) correlates most strongly with neutral genetic variation and so is best explained by historical processes, (2) reflects selection associated with different visual environments (dense versus open habitats) and/or (3) reflects selection associated with climatic variation. LOCATION: Eastern Australia. METHODS: We quantified colour variation using reflectance spectrometry and visual models. We performed geographical cline analysis of colour and neutral genetic variation (genomeâwide single nucleotide polymorphisms). We tested for correlations of colour variation with climate, vegetation density, geographical location and genetic variation. We accounted for covariation and spatial autocorrelation, and conducted analyses at continental and regional spatial scales. RESULTS: Clinal variation of colour traits and neutral genetic markers were largely concordant. At the continental scale, colour variation was strongly associated with neutral genetic structure and geography, and to a lesser extent with environment. At the regional scale, environmental variation was a better predictor of colour variation than it was at the larger scale. MAIN CONCLUSION: At the continental scale, colour variation is strongly associated with largeâscale population history. In contrast, at the regional scale, where the influence of history and geography is weaker, environmental variation has a role in facilitating the maintenance of colour variation. Our results highlight the need to assess selective and neutral alternatives at multiple spatial scales when studying geographical variation.

Parrots (Order: Psittaciformes) are a diverse clade that is easily distinguishable from other birds. Despite the clear characters that define Psittaciformes (hooked bills, zygodactylous feet, and plumage that is often predominantly green or red), relative morphological uniformity among parrots has made taxonomic classification a fraught endeavor for over a century. Parrot systematics were propelled forward when DNA sequencing data shed insights into higher- and species-level relationships. However, despite these significant advances, major gaps in taxon sampling and uncertainty in relationships remained due to inferring phylogenetic relationships with short fragments of DNA. Recent work using genome-wide molecular markers with nearly complete parrot species-level sampling has brought clarity to many of the remaining outstanding questions on taxonomic relationships. Here, we build on this work by including four additional species to present a taxonomic revision of Psittaciformes better aligned with its evolutionary tree. We infer maximum likelihood and time-calibrated phylogenies for parrots, present accounts for 106 genera, compare how our findings relate to previous work, and highlight future areas of research. The family-group nomenclature we propose reflects deep evolutionary divergences with diagnosable synapomorphies that are commensurate across comparable ranks in psittaciform clades. We erect three new family-group names at the rank of tribe (Brotogerini Smith, Thom, and Joseph, 2024; Neophemini Schodde, Mason, Smith, Thom, and Joseph, 2024; Bolbopsittacini Smith, Thom, and Joseph, 2024). We elevate one tribe to subfamily rank for the cacatuid genus Probosciger and we restrict usage of the recently introduced tribe Touitini to its type genus Touit. At shallower taxonomic scales, recognition of more rather than fewer genera addresses issues of paraphyly or high discordance in morphological and genomic characters at those levels. We support many reinstatements of older generic names advocated in recent decades, and we further reinstate five valid, available generic names not widely used in recent literature if at all (Licmetis, Gymnopsittacus, Clarkona, Suavipsitta, Cardeos). We advocate the retention of Vini Lesson, 1833, over Coriphilus Wagler, 1832, based on preliminary examination showing substantially more frequent usage of the former. We redraw generic limits in some other cases (e.g., Bolborhynchus parrotlets and allies) and this includes recognizing fewer genera than recently proposed for the Psittacula sensu lato ringneck parakeets. Our revised classification of parrots addresses many longstanding taxonomic questions including those that have arisen through the acquisition of genetic data. It provides context for the temporal origins of psittaciform clades and the taxonomic and phenotypic diversification throughout their evolutionary history. We hope that it will be a benchmark guiding further taxonomic study as well as for downstream analyses in many other fields. [ABSTRACT FROM AUTHOR]

Species diversification often results from divergent evolution of ecological or social signaling traits. Theoretically, a combination of the two may promote speciation, however, empirical examples studying how social signal and ecological divergence might be involved in diversification are rare in general and typically do not consider range overlap as a contributing factor. We show that ecologically distinct lineages within the Australian sand dragon species complex (including Ctenophorus maculatus, Ctenophorus fordi, and Ctenophorus femoralis) have diversified recently, diverging in ecologically relevant and social signaling phenotypic traits as arid habitats expanded and differentiated. Diversification has resulted in repeated and independent invasion of distinct habitat types, driving convergent evolution of similar phenotypes. Our results suggest that parapatry facilitates diversification in visual signals through reinforcement as a hybridization-avoidance mechanism. We show that particularly striking variation in visual social signaling traits is better explained by the extent of lineage parapatry relative to ecological or phylogenetic divergence, suggesting that these traits reinforce divergence among lineages initiated by ecologically adaptive evolution. This study provides a rare empirical example of a repeated, intricate relationship between ecological and social signal evolution during diversification driven by ecological divergence and the evolution of new habitats, thereby supporting emergent theories regarding the importance of both ecological and social trait evolution throughout speciation.

The south-western land division of Western Australia (SWWA), bordering the temperate Southern and Indian Oceans, is the only global biodiversity hotspot recognised in Australia. Renowned for its extraordinary diversity of endemic plants, and for some of the largest and most botanically significant temperate heathlands and woodlands on Earth, SWWA has long fascinated biogeographers. Its flat, highly weathered topography and the apparent absence of major geographic factors usually implicated in biotic diversification have challenged attempts to explain patterns of biogeography and mechanisms of speciation in the region. Botanical studies have always been central to understanding the biodiversity values of SWWA, although surprisingly few quantitative botanical analyses have allowed for an understanding of historical biogeographic processes in both space and time. Faunistic studies, by contrast, have played little or no role in defining hotspot concepts, despite several decades of accumulating quantitative research on the phylogeny and phylogeography of multiple lineages. In this review we critically analyse datasets with explicit supporting phylogenetic data and estimates of the time since divergence for all available elements of the terrestrial fauna, and compare these datasets to those available for plants. In situ speciation has played more of a role in shaping the south-western Australian fauna than has long been supposed, and has occurred in numerous endemic lineages of freshwater fish, frogs, reptiles, snails and less-vagile arthropods. By contrast, relatively low levels of endemism are found in birds, mammals and highly dispersive insects, and in situ speciation has played a negligible role in generating local endemism in birds and mammals. Quantitative studies provide evidence for at least four mechanisms driving patterns of endemism in south-western Australian animals, including: (i) relictualism of ancient Gondwanan or Pangaean taxa in the High Rainfall Province; (ii) vicariant isolation of lineages west of the Nullarbor divide; (iii) in situ speciation; and (iv) recent population subdivision. From dated quantitative studies we derive four testable models of historical biogeography for animal taxa in SWWA, each explicit in providing a spatial, temporal and topological perspective on patterns of speciation or divergence. For each model we also propose candidate lineages that may be worthy of further study, given what we know of their taxonomy, distributions or relationships. These models formalise four of the strongest patterns seen in many animal taxa from SWWA, although other models are clearly required to explain particular, idiosyncratic patterns. Generating numerous new datasets for suites of co-occurring lineages in SWWA will help refine our understanding of the historical biogeography of the region, highlight gaps in our knowledge, and allow us to derive general postulates from quantitative (rather than qualitative) results. For animals, this process has now begun in earnest, as has the process of taxonomically documenting many of the more diverse invertebrate lineages. The latter remains central to any attempt to appreciate holistically biogeographic patterns and processes in SWWA, and molecular phylogenetic studies should - where possible - also lead to tangible taxonomic outcomes.

Abstract Data on dental practices related to caries risk assessment (CRA) are scarce among Brazilian dentists. This study aimed to determine the prevalence of CRA use by dentists and factors associated with its use, as well as to quantify dentists’ ratings of the importance of specific factors when treatment planning. Dentists registered at the Regional Council of Dentistry of São Paulo State – Araraquara region were sent two paper questionnaires that comprised: a) characteristics of dentists themselves, their practices, and their patients; and b) the translated version of the “Assessment of Caries Diagnosis and Caries Treatment” Questionnaire from the U.S. National Dental Practice-Based Research Network. Participants were 206 dentists who currently practiced in Araraquara and treated dental caries. Descriptive statistics and multiple logistic regression analyses were used for data analysis. Thirty-six percent of the dentists reported they perform CRA and, among them, 36% indicated they record the assessment on a special form that is kept in the patient chart. More years since dental school graduation (OR = 1.1, p = 0.002) and holding an advanced academic degree (OR=2.6, p=0.005) were associated with a higher likelihood of performing CRA, whereas exclusively using a private practice model (OR = 0.5, p = 0.016) was associated with a lower likelihood of performing CRA. The current oral hygiene and commitment to return for follow-up were the most important risk factors for treatment planning. In conclusion, CRA was not a routine procedure in daily practice among the majority of participating dentists. Specific demographic, practice and academic education characteristics were associated with performing CRA.