Introduction The 2009 Family Smoking Prevention and Tobacco Control Act banned characterizing flavors other than menthol in cigarettes but did not restrict their use in other forms of tobacco (e.g., ...smokeless, cigars, hookah, e-cigarettes). Methods A cross-sectional analysis of Wave 1 data from 45,971 U.S. adults and youth, aged ≥12 years in the Population Assessment of Tobacco and Health (PATH) Study collected in 2013–2014, was conducted in 2016. This study examined (1) the prevalence and reasons for use of flavored tobacco products; (2) the proportion of ever tobacco users reporting that their first product was flavored; and (3) correlates of current flavored tobacco product use. Results Current flavored (including menthol) tobacco product use was highest in youth (80%, aged 12–17 years); and young adult tobacco users (73%, aged 18–24 years); and lowest in older adult tobacco users aged ≥65 years (29%). Flavor was a primary reason for using a given tobacco product, particularly among youth. Eighty-one percent of youth and 86% of young adult ever tobacco users reported that their first product was flavored versus 54% of adults aged ≥25 years. In multivariable models, reporting that one’s first tobacco product was flavored was associated with a 13% higher prevalence of current tobacco use among youth ever tobacco users and a 32% higher prevalence of current tobacco use among adult ever users. Conclusions These results add to the evidence base that flavored tobacco products may attract young users and serve as starter products to regular tobacco use.
Abstract Avian feather lice (Phthiraptera: Ischnocera) have undergone morphological diversification into ecomorphs based on how they escape host preening defences. Parrot lice are one prominent ...example of this phenomenon, with wing, body, or head louse ecomorphs occurring on various groups of parrots. Currently defined genera of parrot lice typically correspond to this ecomorphological variation. Here we explore the phylogenetic relationships among parrot feather lice by sequencing whole genomes and assembling a target set of 2395 nuclear protein coding genes. Phylogenetic trees based on concatenated and coalescent analyses of these data reveal highly supported trees with strong agreement between methods of analysis. These trees reveal that parrot feather lice fall into two separate clades that form a grade with respect to the Brueelia-complex. All parrot louse genera sampled by more than one species were recovered as monophyletic. The evolutionary relationships among these lice showed evidence of strong biogeographic signal, which may also be related to the relationships among their hosts.
Parasite dispersal can shape host–parasite interactions at both deep and shallow timescales. One approach to understanding the effects of dispersal is to study parasite lineages that differ in ...dispersal capability but are from the same group of hosts. In this study, we compared phylogenetic and population genetic patterns of wing and body lice from ground‐doves. Wing lice are more capable of dispersal than body lice. We sequenced full genomes of individual lice for multiple representatives of several wing and body louse species. From these data, we assembled genes for phylogenetic analysis and called SNPs for population genetic analysis. At the phylogenetic level, body lice showed more codivergence with their hosts than did wing lice. However, both wing and body lice exhibited some phylogenetic congruence with their hosts. Within species, body lice showed more population genetic structure than wing lice, although both types of lice showed some structure according to biogeography. Body lice also had significantly lower heterozygosity than wing lice, suggesting more inbreeding. Our results demonstrate that dispersal can shape a host–parasite system across evolutionary time, but also that other factors (e.g., host association and biogeography) can have varying degrees of influence on different groups of parasites and at different evolutionary scales.
Abstract
The insect order Psocodea is a diverse lineage comprising both parasitic (Phthiraptera) and nonparasitic members (Psocoptera). The extreme age and ecological diversity of the group may be ...associated with major genomic changes, such as base compositional biases expected to affect phylogenetic inference. Divergent morphology between parasitic and nonparasitic members has also obscured the origins of parasitism within the order. We conducted a phylogenomic analysis on the order Psocodea utilizing both transcriptome and genome sequencing to obtain a data set of 2370 orthologous genes. All phylogenomic analyses, including both concatenated and coalescent methods suggest a single origin of parasitism within the order Psocodea, resolving conflicting results from previous studies. This phylogeny allows us to propose a stable ordinal level classification scheme that retains significant taxonomic names present in historical scientific literature and reflects the evolution of the group as a whole. A dating analysis, with internal nodes calibrated by fossil evidence, suggests an origin of parasitism that predates the K-Pg boundary. Nucleotide compositional biases are detected in third and first codon positions and result in the anomalous placement of the Amphientometae as sister to Psocomorpha when all nucleotide sites are analyzed. Likelihood-mapping and quartet sampling methods demonstrate that base compositional biases can also have an effect on quartet-based methods.Illumina; Phthiraptera; Psocoptera; quartet sampling; recoding methods.
Celotno besedilo
Dostopno za:
DOBA, IZUM, KILJ, NUK, PILJ, PNG, SAZU, SIK, UILJ, UKNU, UL, UM, UPUK
Next-generation sequencing technologies are revolutionizing the fields of genomics, phylogenetics, and population genetics. These new genomic approaches have been extensively applied to a major group ...of parasites, the lice (Insecta: Phthiraptera) of birds and mammals. Two louse genomes have been assembled and annotated to date, and these have opened up new resources for the study of louse biology. Whole genome sequencing has been used to assemble large phylogenomic datasets for lice, incorporating sequences of thousands of genes. These datasets have provided highly supported trees at all taxonomic levels, ranging from relationships among the major groups of lice to those among closely related species. Such approaches have also been applied at the population scale in lice, revealing patterns of population subdivision and inbreeding. Finally, whole genome sequence datasets can also be used for additional study beyond that of the louse nuclear genome, such as in the study of mitochondrial genome fragmentation or endosymbiont function.
Schizophrenia genome-wide association studies have identified >150 regions of the genome associated with disease risk, yet there is little evidence that coding mutations contribute to this disorder. ...To explore the mechanism of non-coding regulatory elements in schizophrenia, we performed ATAC-seq on adult prefrontal cortex brain samples from 135 individuals with schizophrenia and 137 controls, and identified 118,152 ATAC-seq peaks. These accessible chromatin regions in the brain are highly enriched for schizophrenia SNP heritability. Accessible chromatin regions that overlap evolutionarily conserved regions exhibit an even higher heritability enrichment, indicating that sequence conservation can further refine functional risk variants. We identify few differences in chromatin accessibility between cases and controls, in contrast to thousands of age-related differential accessible chromatin regions. Altogether, we characterize chromatin accessibility in the human prefrontal cortex, the effect of schizophrenia and age on chromatin accessibility, and provide evidence that our dataset will allow for fine mapping of risk variants.
•Next-generation sequencing has greatly increased the size of phylogenetic datasets.•Genome reduction approaches are economical, but have limitations.•Full genome sequencing is now feasible for many ...insect groups.•Individual gene sequences can be locally assembled from genomic reads.
Next-generation sequencing technologies provide a substantial increase in the size of molecular phylogenetic datasets that can be obtained for studies of insect systematics. Several new genome reduction approaches are leveraging these technologies to generate large phylogenomic datasets: targeted amplicon sequencing, target capture, and transcriptome sequencing. Although cost effective, these approaches provide limited data for questions outside of phylogenetics. For many groups of insects, sequencing the entire genome at modest coverage is feasible. Using these genomic reads, an automated Target Restricted Assembly Method (aTRAM) can use the results of blast searches to assemble thousands of single copy ortholog genes across a group of interest. These locally assembled genes can then be compiled into very large phylogenomic datasets. These genomic libraries have the advantage in that they also contain reads from the mitochondrial genome and symbiont genomes, as well the entire insect genome, and can be leveraged for additional studies beyond phylogenetics.
Phylogenomics and the evolution of hemipteroid insects Johnson, Kevin P.; Dietrich, Christopher H.; Friedrich, Frank ...
Proceedings of the National Academy of Sciences,
12/2018, Letnik:
115, Številka:
50
Journal Article
Recenzirano
Odprti dostop
Hemipteroid insects (Paraneoptera), with over 10% of all known insect diversity, are a major component of terrestrial and aquatic ecosystems. Previous phylogenetic analyses have not consistently ...resolved the relationships among major hemipteroid lineages. We provide maximum likelihood-based phylogenomic analyses of a taxonomically comprehensive dataset comprising sequences of 2,395 single-copy, protein-coding genes for 193 samples of hemipteroid insects and outgroups. These analyses yield a well-supported phylogeny for hemipteroid insects. Monophyly of each of the three hemipteroid orders (Psocodea, Thysanoptera, and Hemiptera) is strongly supported, as are most relationships among suborders and families. Thysanoptera (thrips) is strongly supported as sister to Hemiptera. However, as in a recent large-scale analysis sampling all insect orders, trees from our data matrices support Psocodea (bark lice and parasitic lice) as the sister group to the holometabolous insects (those with complete metamorphosis). In contrast, four-cluster likelihood mapping of these data does not support this result. A molecular dating analysis using 23 fossil calibration points suggests hemipteroid insects began diversifying before the Carboniferous, over 365 million years ago. We also explore implications for understanding the timing of diversification, the evolution of morphological traits, and the evolution of mitochondrial genome organization. These results provide a phylogenetic framework for future studies of the group.
Parasites and other symbionts are crucial components of ecosystems, regulating host populations and supporting food webs. However, most symbiont systems, especially those involving commensals and ...mutualists, are relatively poorly understood. In this study, we have investigated the nature of the symbiotic relationship between birds and their most abundant and diverse ectosymbionts: the vane‐dwelling feather mites. For this purpose, we studied the diet of feather mites using two complementary methods. First, we used light microscopy to examine the gut contents of 1,300 individual feather mites representing 100 mite genera (18 families) from 190 bird species belonging to 72 families and 19 orders. Second, we used high‐throughput sequencing (HTS) and DNA metabarcoding to determine gut contents from 1,833 individual mites of 18 species inhabiting 18 bird species. Results showed fungi and potentially bacteria as the main food resources for feather mites (apart from potential bird uropygial gland oil). Diatoms and plant matter appeared as rare food resources for feather mites. Importantly, we did not find any evidence of feather mites feeding upon bird resources (e.g., blood, skin) other than potentially uropygial gland oil. In addition, we found a high prevalence of both keratinophilic and pathogenic fungal taxa in the feather mite species examined. Altogether, our results shed light on the long‐standing question of the nature of the relationship between birds and their vane‐dwelling feather mites, supporting previous evidence for a commensalistic–mutualistic role of feather mites, which are revealed as likely fungivore–microbivore–detritivore symbionts of bird feathers.
Evolution results from the interaction of stochastic and deterministic processes that create a web of historical contingency, shaping gene content and organismal function. To understand the scope of ...this interaction, we examine the relative contributions of stochasticity, determinism, and contingency in shaping gene inactivation in 34 lineages of endosymbiotic bacteria, Sodalis, found in parasitic lice, Columbicola, that are independently undergoing genome degeneration. Here we show that the process of genome degeneration in this system is largely deterministic: genes involved in amino acid biosynthesis are lost while those involved in providing B-vitamins to the host are retained. In contrast, many genes encoding redundant functions, including components of the respiratory chain and DNA repair pathways, are subject to stochastic loss, yielding historical contingencies that constrain subsequent losses. Thus, while selection results in functional convergence between symbiont lineages, stochastic mutations initiate distinct evolutionary trajectories, generating diverse gene inventories that lack the functional redundancy typically found in free-living relatives.
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