Combined Analysis of Extant Rhynchonellida (Brachiopoda) using Morphological and Molecular Data.

Independent molecular and morphological phylogenetic analyses have often produced discordant results for certain groups which, for fossil-rich groups, raises the possibility that morphological data might mislead in those groups for which we depend upon morphology the most. Rhynchonellide brachiopods, with more than 500 extinct genera but only 19 extant genera represented today, provide an opportunity to explore the factors that produce contentious phylogenetic signal across datasets, as previous phylogenetic hypotheses generated from molecular sequence data bear little agreement with those constructed using morphological characters. Using a revised matrix of 66 morphological characters, and published ribosomal DNA sequences, we performed a series of combined phylogenetic analyses to identify conflicting phylogenetic signals. We completed a series of parsimony-based and Bayesian analyses, varying the data used, the taxa included, and the models used in the Bayesian analyses. We also performed simulation-based sensitivity analyses to assess whether the small size of the morphological data partition relative to the molecular data influenced the results of the combined analyses. In order to compare and contrast a large number of phylogenetic analyses and their resulting summary trees, we developed a measure for the incongruence between two topologies and simultaneously ignore any differences in phylogenetic resolution. Phylogenetic hypotheses generated using only morphological characters differed among each other, and with previous analyses, whereas molecular-only and combined Bayesian analyses produced extremely similar topologies. Characters historically associated with traditional classification in the Rhynchonellida have very low consistency indices on the topology preferred by the combined Bayesian analyses. Overall, this casts doubt on the use of morphological systematics to resolve relationships among the crown rhynchonellide brachiopods. However, expanding our dataset to a larger number of extinct taxa with intermediate morphologies is necessary to exclude the possibility that the morphology of extant taxa is not dominated by convergence along long branches.

Flutracking weekly online community survey of influenza-like illness annual report, 2015.

Flutracking is a national online community influenza-like illness (ILI) surveillance system that monitors weekly ILI activity and impact in the Australian community. This article reports on the 2015 findings from Flutracking. From 2014 to 2015 there was a 38.5% increase in participants to 27,824 completing at least 1 survey with a peak weekly response of 25,071 participants. The 2015 Flutracking national ILI weekly fever and cough percentages peaked in late August at 5.0% in the unvaccinated group, in the same week as the national counts of laboratory confirmed influenza peaked. A similar percentage of Flutracking participants took two or more days off from work or normal duties in 2015 (peak level 2.3%) compared with 2014 (peak level 2.5%) and the peak weekly percentage of participants seeking health advice was 1.6% in both 2014 and 2015. Flutracking fever and cough peaked in the same week as Influenza Complications Alert Network surveillance system influenza hospital admissions. The percentage of Flutracking participants aged 5 to 19 years with cough and fever in 2015 was the highest since 2011. The 2015 season was marked by a transition to predominantly influenza B strain circulation, which particularly affected younger age groups. However, for those aged 20 years and over, the 2015 national Flutracking influenza season was similar to 2014 in community ILI levels and impact.

Flutracking weekly online community survey of influenza-like illness: 2013 and 2014.

Flutracking is a national online community influenza-like illness (ILI) surveillance system that monitors weekly ILI activity and field vaccine effectiveness. This article reports on the 2013 and 2014 findings from Flutracking. From 2013 to 2014 there was a 14.0% increase in participants who completed at least 1 survey to 21,021 participants. By the end of the 2013 and 2014 seasons, respectively 59.7% and 59.1% of all participants had received the seasonal influenza vaccine. The 2013 Flutracking national ILI weekly incidence peaked in late August at 4.3% in the unvaccinated group, 1 week earlier than national counts of laboratory confirmed influenza. The 2014 Flutracking national ILI weekly incidence also peaked in late August at 4.7% in the unvaccinated group, in the same week as national counts of laboratory confirmed influenza. A lower percentage of Flutracking participants took two or more days off from work or normal duties in 2013 (peak level 1.6%) compared with 2014 (peak level 2.5%) and sought health advice in 2013 (peak level of 1.1%) compared with 2014 (peak of 1.6%). Flutracking ILI surveillance suggests that 2014 was a moderately more intense season than 2013 and similar to 2012.

Building influenza surveillance pyramids in near real time, Australia.

A timely measure of circulating influenza virus severity has been elusive. Flutracking, the Australian online influenza-like illness surveillance system, was used to construct a surveillance pyramid in near real time for 2011/2012 participants and demonstrated a striking difference between years. Such pyramids will facilitate rapid estimation of attack rates and disease severity.

Flutracking weekly online community survey of influenza-like illness annual report 2011 and 2012.

Flutracking is a national online community influenza-like illness (ILI) surveillance system that monitors weekly ILI activity and field vaccine effectiveness (FVE). This article reports on the 2011 and 2012 findings from Flutracking. There was a 22% increase in participants to 16,046 who completed at least one survey in 2012, compared with 2011 (13,101). By October 2012 (the end of the 2012 season), 54.2% of participants had received the 2012 seasonal vaccine, while by the end of the 2011 season, 55.9% of participants had received the 2011 seasonal vaccine. From 2007 to 2012 the FVE calculation for New South Wales participants demonstrated that the seasonal vaccine was effective except in 2009 when a novel H1N1 virus was dominant. The 2012 Flutracking ILI weekly incidence peaked in mid-July at 4.9% in the unvaccinated group, 1 month earlier than laboratory confirmed influenza. The 2011 Flutracking ILI weekly incidence peaked in mid-August at 4.1% in the unvaccinated group, 1 week later than laboratory confirmed influenza. Similar to laboratory notifications, there was an increase in ILI activity from 2010 to 2012, with the peak weekly ILI prevalence for 2012 Flutracking data, (unstratified by vaccination status), being higher (4.7%) than the peak weekly prevalence for 2011 (3.8%) and 2010 (3.7%). The 2012 Flutracking influenza season showed moderate levels of ILI, compared with lower levels of ILI seen in 2011 and 2010, and consistent with the increase in national influenza laboratory notifications.

FluTracking: Weekly online community-based surveillance of influenza-like illness in Australia, 2019 Annual Report.

Abstract: FluTracking provided evidence for an early, long, but moderate influenza season in the Australian community compared to prior years. Influenza-like illness (ILI) activity in 2019 peaked earlier (week ending 16 June) than any season on record in FluTracking data. ILI attack rates were above average early in the 2019 season (peak of 2.2%), and the duration of peak activity was longer than most prior years. However, ILI attack rates were lower than the five-year average in the latter half of the season. FluTracking participants reported higher vaccination coverage in 2019 (73.3%) compared with 2018 (65.7%), with the most notable increase in children aged less than five years (69.3% in 2019, compared to 55.6% in 2018). The total 2019 count of laboratory notifications (312,945) was higher than prior years (2007 onwards), and the peak weekly count of 18,429 notifications in 2019 was also higher than all prior years, except 2017. FluTracking makes a comparison to another surveillance system each year. The peak weekly percentage of calls to HealthDirect that were influenza-related was higher in 2019 (12.8%) than for 2014-2018 (range of 8.2-11.4% for peak week of activity each year). FluTracking participants reported a 2.5 times increase in influenza testing from 2018 to 2019 and a 1.5 times increase from 2017. Although 2019 was of higher activity and severity than 2018, Flutracking data indicates that 2019 was a lower activity and severity season than 2017, and notifications and influenza-related calls were heightened by increased community concern and testing.

Online Flutracking survey of influenza-like illness during pandemic (H1N1) 2009, Australia.

We compared the accuracy of online data obtained from the Flutracking surveillance system during pandemic (H1N1) 2009 in Australia with data from other influenza surveillance systems. Flutracking accurately identified peak influenza activity timing and community influenza-like illness activity and was significantly less biased by treatment-seeking behavior and laboratory testing protocols than other systems.

Elucidating user behaviours in a digital health surveillance system to correct prevalence estimates.

Estimating seasonal influenza prevalence is of undeniable public health importance, but remains challenging with traditional datasets due to cost and timeliness. Digital epidemiology has the potential to address this challenge, but can introduce sampling biases that are distinct to traditional systems. In online participatory health surveillance systems, the voluntary nature of the data generating process must be considered to address potential biases in estimates. Here we examine user behaviours in one such platform, FluTracking, from 2011 to 2017. We build a Bayesian model to estimate probabilities of an individual reporting in each week, given their past reporting behaviour, and to infer the weekly prevalence of influenza-like-illness (ILI) in Australia. We show that a model that corrects for user behaviour can substantially affect ILI estimates. The model examined here elucidates several factors, such as the status of having ILI and consistency of prior reporting, that are strongly associated with the likelihood of participating in online health surveillance systems. This framework could be applied to other digital participatory health systems where participation is inconsistent and sampling bias may be of concern.

Testing Species Assignments in Extant Terebratulide Brachiopods: A Three-dimensional Geometric Morphometric Analysis of Long-Looped Brachidia.

Species of terebratulide brachiopods have been largely characterized qualitatively on the basis of morphology. Furthermore, species-level morphological variability has rarely been analyzed within a quantitative framework. The objective of our research is to quantify morphological variation to test the validity of extant named species of terebratulide brachiopods, focusing on the lophophore-supporting structures-the "long loops." Long loops are the most distinctive and complex morphological feature in terebratellidine brachiopods and are considered to be phylogenetically and taxonomically informative. We studied eight species with problematic species identities in three genera distributed in the North Pacific: Laqueus, Terebratalia, and Dallinella. Given how geometrically complex long loops are, we generated 3D models from computed tomography (CT) scans of specimens of these eight species and analyzed them using 3D geometric morphometrics. Our goal was to determine ranges of variation and to test whether species are clearly distinguishable from one another in morphospace and statistically. Previous studies have suggested that some species might be overly split and are indistinguishable. Our results show that these extant species of terebratellidines can be reliably distinguished on the basis of quantitative loop morphometrics. Using 3D geometric morphometric methods, we demonstrate the utility of CT beyond purely descriptive imaging purposes in testing the morphometric validity of named species. It is crucial to treat species described and named from qualitative morphology as working hypotheses to be tested; many macroevolutionary studies depend upon the accurate assessment of species in order to identify and seek to explain macroevolutionary patterns. Our results provide quantitative documentation of the distinction of these species and thus engender greater confidence in their use to characterize macroevolutionary patterns among extant terebratellidine brachiopods. These methods, however, require further testing in extinct terebratellidines, which only rarely preserve the delicate long loop in three dimensions. In addition, molecular analyses of extant terebratellidines will test the species delimitations supported by the morphometric analyses presented in this study. [Species determination; morphological variability; 3D geometric morphometrics; terebratulide brachiopods; long loops.].

Flutracking weekly online community survey of influenza-like illness annual report, 2016

Flutracking is a national online community influenza-like illness (ILI) surveillance system that monitors weekly ILI attack rates and seriousness of disease in the Australian community. This article reports on the 2016 findings. From 2015 to 2016 there was an 11.4% increase in participants to 30,998 completing at least one survey with a peak weekly response of 27,094 participants and a minimum weekly response of 26,123. The 2016 Flutracking national weekly percentage of participants with fever and cough peaked in late August at 2.7%, one week earlier than the national counts of laboratory confirmed influenza peaked. A lower percentage of participants took 2 or more days off from work or normal duties and sought medical advice in 2016 (peak level 1.6% and 1.0% respectively) compared with 2015 (peak level 2.0% and 1.3% respectively). Flutracking fever and cough peaked in the same week as death rates for influenza and pneumonia recorded by the NSW Registry of Births, Deaths and Marriages. The percentage of participants aged 0 to 14 years with cough and fever was higher than all other age groups in 2016. Overall, Flutracking surveillance demonstrated that the attack rates and seriousness of disease for the 2016 season at the community level were lower than 2015 and 2014.

Accounting for Healthcare-Seeking Behaviours and Testing Practices in Real-Time Influenza Forecasts.

For diseases such as influenza, where the majority of infected persons experience mild (if any) symptoms, surveillance systems are sensitive to changes in healthcare-seeking and clinical decision-making behaviours. This presents a challenge when trying to interpret surveillance data in near-real-time (e.g., to provide public health decision-support). Australia experienced a particularly large and severe influenza season in 2017, perhaps in part due to: (a) mild cases being more likely to seek healthcare; and (b) clinicians being more likely to collect specimens for reverse transcription polymerase chain reaction (RT-PCR) influenza tests. In this study, we used weekly Flutracking surveillance data to estimate the probability that a person with influenza-like illness (ILI) would seek healthcare and have a specimen collected. We then used this estimated probability to calibrate near-real-time seasonal influenza forecasts at each week of the 2017 season, to see whether predictive skill could be improved. While the number of self-reported influenza tests in the weekly surveys are typically very low, we were able to detect a substantial change in healthcare seeking behaviour and clinician testing behaviour prior to the high epidemic peak. Adjusting for these changes in behaviour in the forecasting framework improved predictive skill. Our analysis demonstrates a unique value of community-level surveillance systems, such as Flutracking, when interpreting traditional surveillance data. These methods are also applicable beyond the Australian context, as similar community-level surveillance systems operate in other countries.

PHYLOGENETIC RELATIONSHIPS AMONG EXTANT BRACHIOPODS.

Abstract- The monophyletic status of the Brachiopoda and phylogenetic relationships within the phylum have long been contentious issues for brachiopod systematists. The relationship of brachiopods to other lophophore-bearing taxa is also uncertain; results from recent morphological and molecular studies are in conflict. To test current hypotheses of relationship, a phylogenetic analysis was completed (using PAUP 3.1.1) with 112 morphological and embryological characters that vary among extant representatives of seven brachiopod superfamilies, using bryozoans, phoronids, pterobranchs and sipunculids as outgroups. In the range of analyses performed, brachiopod monophyly is well supported, particularly by characters of soft anatomy. Arguments concerning single or multiple origins of a bivalved shell are not relevant to recognizing brachiopods as a clade. Articulate monophyly is very strongly supported, but inarticulate monophyly receives relatively weak support. Unlike previous studies, the nature of uncertainties about the clade status of Inarticulata are detailed explicitly here, making them easier to test in the future. Calcareous inarticulates appear to share derived characters with the other inarticulates, while sharing many primitive characters with other calcareous brachiopods (the articulates). Experimental manipulation of the data matrix reveals potential sources of bias in previous hypotheses of brachiopod phylogeny. Although not tested explicitly, lophophorate monophyly is very tentatively supported. Molecular systematic studies of a diverse group of brachiopods and other lophophorates will be particularly welcome in providing a test of the conclusions presented here.

Flutracking weekly online community survey of influenza-like illness annual report, 2010.

Flutracking is a national weekly online survey of influenza-like illness (ILI) completed by community members. Flutracking integrates participants' ILI symptom information with their influenza vaccination status to monitor influenza activity and field vaccine effectiveness (FVE). This report summarises results from the 2010 Flutracking season compared with previous seasons. Nationally, participation in Flutracking has more than doubled between 2008 and 2010, with 5,346 new participants enrolled or recruited in 2010 and a peak weekly participation of 10,773. By the end of the 2010 season, 5,904 of 9,109 (64.8%) participants had received the monovalent pandemic vaccine and/or the 2010 seasonal vaccine. From 2007 to 2010 FVE calculations demonstrated that the seasonal vaccine was effective except in 2009 during the pandemic. Peak 2010 ILI activity occurred in early June and August, and peak weekly 2010 ILI rates (4.2% among unvaccinated participants) were lower than the peak ILI rates during the 2009 pandemic (6.0% among unvaccinated participants). However, the decrease in laboratory notifications was much larger than the decrease in Flutracking rates. In summary, the number of Flutracking participants continued to steadily increase over the 2010 influenza season. The system has shown value in providing weekly vaccination uptake data during and beyond the 2009 influenza pandemic, as well as rapid FVE estimates that are qualitatively aligned with findings from other analyses of vaccine efficacy. Flutracking has also provided estimates of weekly community ILI activity that were not biased by health seeking behaviour and clinician testing practices.

Flutracking provides a measure of field influenza vaccine effectiveness, Australia, 2007-2009.

We reviewed Flutracking's (an Australian weekly online survey of community members) performance in estimating influenza vaccine effectiveness using New South Wales data for participants aged 18-60 years of age from 2007, 2008 and 2009. Flutracking results were consistent with previous findings that the 2009 seasonal influenza vaccine was ineffective in preventing the dominant pH1N109 strain of influenza, and that 2007 and 2008 vaccine strains were considered well matched to the circulating virus in Australia. Flutracking may offer an opportunity to estimate real time vaccine effectiveness during an influenza season.