CALIBRATING DIVERGENCE TIMES ON SPECIES TREES VERSUS GENE TREES: IMPLICATIONS FOR SPECIATION HISTORY OF APHELOCOMA JAYS

Estimates of the timing of divergence are central to testing the underlying causes of speciation. Relaxed molecular clocks and fossil calibration have improved these estimates; however, these advances are implemented in the context of gene trees, which can overestimate divergence times. Here we couple recent innovations for dating speciation events with the analytical power of species trees, where multilocus data are considered in a coalescent context. Divergence times are estimated in the bird genus Aphelocoma to test whether speciation in these jays coincided with mountain uplift or glacial cycles. Gene trees and species trees show general agreement that diversification began in the Miocene amid mountain uplift. However, dates from the multilocus species tree are more recent, occurring predominately in the Pleistocene, consistent with theory that divergence times can be significantly overestimated with gene-tree based approaches that do not correct for genetic divergence that predates speciation. In addition to coalescent stochasticity, Haldane's rule could account for some differences in timing estimates between mitochondrial DNA and nuclear genes. By incorporating a fossil calibration applied to the species tree, in addition to the process of gene lineage coalescence, the present approach provides a more biologically realistic framework for dating speciation events, and hence for testing the links between diversification and specific biogeographic and geologic events.Peer Reviewedhttp://deepblue.lib.umich.edu/bitstream/2027.42/79292/1/j.1558-5646.2010.01097.x.pd

New and improved demonstrations, each illustrating a single scientific paper

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A 16S rRNA gene and draft genome database for the murine oral bacterial community

A curated murine oral microbiome database to be used as a reference for mouse-based studies has been constructed using a combination of bacterial culture, 16S rRNA gene amplicon, and whole-genome sequencing. The database comprises a collection of nearly full-length 16S rRNA gene sequences from cultured isolates and draft genomes from representative taxa collected from a range of sources, including specific-pathogen-free laboratory mice, wild Mus musculus domesticus mice, and formerly wild wood mouse Apodemus sylvaticus. At present, it comprises 103 mouse oral taxa (MOT) spanning four phyla—Firmicutes, Proteobacteria, Actinobacteria, and Bacteroidetes—including 12 novel undescribed species-level taxa. The key observations from this study are (i) the low diversity and predominantly culturable nature of the laboratory mouse oral microbiome and (ii) the identification of three major murine-specific oral bacterial lineages, namely, Streptococcus danieliae (MOT10), Lactobacillus murinus (MOT93), and Gemella species 2 (MOT43), which is one of the novel, still-unnamed taxa. Of these, S. danieliae is of particular interest, since it is a major component of the oral microbiome from all strains of healthy and periodontally diseased laboratory mice, as well as being present in wild mice. It is expected that this well-characterized database should be a useful resource for in vitro experimentation and mouse model studies in the field of oral microbiology

Radiocarbon evidence for the stability of polar ocean overturning during the Holocene

Funding: T.C. acknowledges support from the Strategic Priority Research Program of Chinese Academy of Sciences (XDB40010200), Fundamental Research Funds for the Central Universities (020614380116) and National Natural Science Foundation of China (41991325, 41822603 and 42021001). L.F.R. acknowledges support from the Natural Environment Research Council (NE/S001743/1, NE/R005117/1, NE/N003861/1 and NE/X00127X/1).Proxy-based studies have linked the pre-industrial atmospheric pCO2 rise of ∼20 ppmv in the mid- to late Holocene to an inferred increase in the Southern Ocean overturning and associated biogeochemical changes. However, the history of polar ocean overturning and ventilation through the Holocene remains poorly constrained, leaving important gaps in the assessment of the feedbacks between changes in ocean circulation and the carbon cycle in a warm climate state. The deep-ocean radiocarbon content, which provides a measure of ventilation, responds to circulation changes on centennial to millennial time scales. Here we present absolutely dated deep-sea coral radiocarbon records from the Drake Passage, between South America and Antarctica, and Reykjanes Ridge, south of Iceland, over the Holocene. Our data suggest that ventilation in the Antarctic circumpolar waters and North Atlantic Deep Water is surprisingly invariant within proxy uncertainties at our sampling resolution. Our findings indicate that long-term, large-scale polar ocean overturning has not been disturbed to a level resolvable by radiocarbon and is probably not responsible for the millennial atmosphere pCO2 evolution through the Holocene. Instead, continuous nutrient and carbon redistribution within the water column following deglaciation, as well as changes in land organic carbon stock, might have regulated atmospheric CO2 budget during this period.Publisher PDFPeer reviewe

An extended computational study of Criegee intermediate - alcohol reactions

High level ab initio calculations (DF-LCCSD(T)-F12a//B3LYP/aug-cc-pVTZ) are performed on a range of stabilized Criegee intermediate (sCI) – alcohol reactions, computing reaction coordinate energies, leading to the formation of α-alkyoxyl-alkyl-hydroperoxides (AAAHs). These potential energy surfaces are used to model bimolecular reaction kinetics over a range of temperatures. The calculations performed in this work reproduce the complicated temperature dependent reaction rates of CH2OO and (CH3)2COO with methanol, which have previously been experimentally determined. This methodology is then extended to compute reaction rates of 22 different Criegee intermediates with methanol, including several intermediates derived from isoprene ozonolysis. In some cases, sCI-alcohol reaction rates approach those of sCI-(H2O)2. This suggests that in regions with elevated alcohol concentrations, such as urban Brazil, these reactions may generate significant quantities of AAAHs, and may begin to compete with sCI reactions with other trace tropospheric pollutants such as SO2. This work also demonstrates the ability of alcohols to catalyse the 1,4-H transfer unimolecular decomposition of α-methyl substituted sCIs

Reinterpreting radiocarbon records in bamboo corals ? New insights from the tropical North Atlantic

Deep-sea bamboo corals (family Isididae) have been used as archives for reconstructing changes in the past ocean. However, uncertainties remain regarding the interpretation of geochemical signals from their organic nodes, specifically the water depth of the signals recorded by the coral. Here we explore this question by measuring radiocarbon (14C) and nitrogen (15N) isotopic compositions of the organic nodes in six bamboo corals collected from the central and eastern tropical Atlantic between 700 m and 2000 m water depth. By comparing coral 14C to measured seawater data, regional shallow-water coral records and climate-model outputs, we find contrasting results between the two regions. Our bamboo coral 14C results from the eastern tropical Atlantic support previous studies that suggest organic node carbon is sourced primarily from the mixed layer of the ocean. By contrast, the 14C of bamboo coral organic nodes from the oligotrophic central Atlantic better correlates with the 14C content of the subsurface deep chlorophyll maximum layer rather than the surface mixed layer. Combined with nitrogen isotope data, this observation suggests that sinking and/or ambient zooplankton feeding on phytoplankton from the deep chlorophyll maximum layer can contribute a significant proportion of the diet of bamboo corals. These results suggest that the carbon source for bamboo corals organic nodes may not always reside in the mixed layer, especially in oligotrophic regions, which has implications for 14C-based age model development in bamboo corals

Fine Mapping of 10q and 18q for Familial Alzheimer's Disease in Caribbean Hispanics

Familial Alzheimer's disease (AD [MIM 104300]) has been a focus of intense investigation, primarily in Caucasian families from Europe and North America families. Although the late-onset form of familial AD, beginning after age 65 years, has been linked to regions on chromosomes 10q and 12p, the specific genetic variants have not yet been consistently identified. Using a unique cohort of families of Caribbean Hispanics ancestry, we screened the genome using 340 markers on 490 family members from 96 families with predominantly late-onset AD. We observed the strongest support for linkage on 18q (LOD=3.14). However, 17 additional markers (chromosomes 1-6, 8, 10, 12, and 14) exceeded a two-point LOD score of 1.0 under the affecteds-only autosomal dominant model or affected sibpair model. As we previously reported the fine-mapping effort on 12p showing modest evidence of linkage, we focused our fine-mapping efforts on two other candidate regions in the current report, namely 10q and 18q. We added 31 family members and eight additional Caribbean Hispanic families to fine map 10q and 18q. With additional microsatellite markers, the evidence for linkage for 18q strengthened near 112 cM, where the two-point LOD score for D18S541 was 3.37 and the highest NPL score in that region was 3.65 (P=0.000177). This narrow region contains a small number of genes expressed in the brain. However, at 10q (134-138 cM), the NPL score decreased from 3.15 (P=0.000486) to 2.1 (P=0.0218), but two broad peaks remained overlapping with previously reported peaks. Our results provide modest support for linkage on 10q and 12p in this cohort of Caribbean Hispanic families with familial Alzheimer's disease, and strong evidence for a new locus on 18

Effect of an Aerosol Box on Intubation in Simulated Emergency Department Airways: A Randomized Crossover Study

Introduction: The use of transparent plastic aerosol boxes as protective barriers during endotracheal intubation has been advocated during the severe acute respiratory syndrome coronavirus 2 pandemic. There is evidence of worldwide distribution of such devices, but some experts have warned of possible negative impacts of their use. The objective of this study was to measure the effect of an aerosol box on intubation performance across a variety of simulated difficult airway scenarios in the emergency department. Methods: This was a randomized, crossover design study. Participants were randomized to intubate one of five airway scenarios with and without an aerosol box in place, with randomization of intubation sequence. The primary outcome was time to intubation. Secondary outcomes included number of intubation attempts, Cormack-Lehane view, percent of glottic opening, and resident physician perception of intubation difficulty. Results: Forty-eight residents performed 96 intubations. Time to intubation was significantly longer with box use than without (mean 17 seconds [range 6-68 seconds] vs mean 10 seconds [range 5-40 seconds], p <0.001). Participants perceived intubation as being significantly more difficult with the aerosol box. There were no significant differences in the number of attempts or quality of view obtained. Conclusion: Use of an aerosol box during difficult endotracheal intubation increases the time to intubation and perceived difficulty across a range of simulated ED patients

Is Persistent Motor or Vocal Tic Disorder a Milder Form of Tourette Syndrome?

BACKGROUND: Persistent motor or vocal tic disorder (PMVT) has been hypothesized to be a forme fruste of Tourette syndrome (TS). Although the primary diagnostic criterion for PMVT (presence of motor or vocal tics, but not both) is clear, less is known about its clinical presentation. OBJECTIVE: The goals of this study were to compare the prevalence and number of comorbid psychiatric disorders, tic severity, age at tic onset, and family history for TS and PMVT. METHODS: We analyzed data from two independent cohorts using generalized linear equations and confirmed our findings using meta‐analyses, incorporating data from previously published literature. RESULTS: Rates of obsessive–compulsive disorder (OCD) and attention deficit hyperactivity disorder (ADHD) were lower in PMVT than in TS in all analyses. Other psychiatric comorbidities occurred with similar frequencies in PMVT and TS in both cohorts, although meta‐analyses suggested lower rates of most psychiatric disorders in PMVT compared with TS. ADHD and OCD increased the odds of comorbid mood, anxiety, substance use, and disruptive behaviors, and accounted for observed differences between PMVT and TS. Age of tic onset was approximately 2 years later, and tic severity was lower in PMVT than in TS. First‐degree relatives had elevated rates of TS, PMVT, OCD, and ADHD compared with population prevalences, with rates of TS equal to or greater than PMVT rates. CONCLUSIONS: Our findings support the hypothesis that PMVT and TS occur along a clinical spectrum in which TS is a more severe and PMVT a less severe manifestation of a continuous neurodevelopmental tic spectrum disorder. © 2021 The Authors. Movement Disorders published by Wiley Periodicals LLC on behalf of International Parkinson and Movement Disorder Societ