Outlier detection methods are still effective even using virtual species created with the probabilistic approach

Liu et al. (Journal of Biogeography, 2018, 45 :164–176) presented an approach to detect outliers in species distribution data by developing virtual species created using the threshold approach. Meynard et al. (Journal of biogeography, 2019, 46 :2141–2144) raised concerns about this approach stating that ‘using a probabilistic approach … may significantly change results’. Here we provide a new series of simulations using the two approaches and demonstrate that the outlier detection approach based on pseudo species distribution models was still effective when using the probabilistic approach, although the detection rate was lower than when using the threshold approach.     

Disturbance does not have a significant impact on waders in an estuary close to conurbations: importance of overlap between birds and people in time and space

Disturbance of wildlife is a potential cause of conservation concern, not least to overwintering waders Charadrii inhabiting estuaries close to conurbations where human recreational and economic activities are often concentrated. Disturbance from people on and alongside intertidal foraging areas could make it more difficult for birds to survive until spring in good condition by reducing the time available for foraging, increasing energy requirements and displacing birds to poorer foraging areas. We adopted a two-part approach to testing whether such significant impacts occurred in a Special Protection Area where disturbance risk was high because of its small size and close proximity to conurbations. In part one, we recorded over the whole estuary during stages of the tidal cycle when part or all of the intertidal zone was exposed and so accessible to waders (i.e. on receding, low and advancing tides): (1) the numbers and activities of people on the intertidal flats and on the adjacent land in those places where people were visible to waders in the intertidal zone and (2) the numbers of waders present and disturbed into flight, the flight distance and flight duration in the ‘overlap’ areas where people did disturb waders. People occurred on < 25% of the 938 ha of intertidal flats, but most waders foraged on mudflats, whereas most people were on sandflats. People on land were visible to foraging waders along < 35% of the 16.5 km of shoreline. Waders and people were therefore substantially separated in space. Within overlap areas, people and waders were often frequently separated in time: for example, people on land mostly disturbed waders when only the upper shore levels were exposed. The average overwintering wader spent < 0.1% of its foraging time during daylight flying away from people and the additional energy expenditure was equivalent to < 0.02% of its daily requirements. The comparison made in part two between our study area and two comparable estuaries showed that the number of visits each day to the overlap areas would need to be 29 or 43 times greater for disturbance to have lowered the birds’ body condition and winter survival. Both parts of the study therefore suggested strongly that the amount of disturbance was too trivial to have a significant impact on waders. It is concluded that: (1) to properly assess disturbance risk to waders, both extensive and intensive observations must be made on the behaviour of people and birds to quantify the extent to which they overlap in space and time, and (2) it should not be assumed that an estuary's close proximity to conurbations, and the presence of large numbers of people in the vicinity of the SPA, necessarily implies a significant disturbance risk to waders.     

Short- and long-term diets of the threatened longhorned pygmy devil ray,Mobula eregoodoo determined using stable isotopes

Most mobulids are listed as near threatened to endangered. Nonetheless, effective conservation measures are hindered by knowledge gaps in their ecology and behaviour. In particular, few studies have assessed diets and trophic ecologies that could inform methods to avoid fishing mortality. Here, a shortfall in data for the longhorned pygmy devil ray, Mobula eregoodoo was addressed by describing temporal variability in dietary preferences using stable isotope analysis. During summer and autumn in 2017, five bather-protection gillnets were deployed off eastern Australia (29° S, 153.5° E). From the catches of these gillnets, 35 adult M. eregoodoo had liver, muscle and stomach contents sampled to determine δ¹³C and δ¹⁵N profiles. Analyses revealed that surface zooplankton and zooplanktivorous teleosts were important dietary components across short- and long-term temporal scales. Large quantities of undigested sandy sprat, Hyperlophus vittatus, in the stomachs of some specimens unequivocally confirm feeding on teleosts. A narrow isotopic niche and minimal isotopic overlap with reef manta rays, Mobula alfredi from the same geographic region in eastern Australia implies M. eregoodoo has unique and highly specialised resource use relative to other mobulids in the area. The species is clearly vulnerable to capture during inshore migrations, presumably where they feed on shallow-water shoaling teleosts. Female M. eregoodoo likely have a low annual reproductive output, so population recoveries from fishing-induced declines are likely to be slow. Measures to reduce the by catch of M. eregoodoo in local bather-protection gillnets, and artisanal fisheries more broadly, should be given priority.     

TMEM106B p.T185S regulates TMEM106B protein levels: implications for frontotemporal dementia

Frontotemporal lobar degeneration (FTLD) is the second leading cause of dementia in individuals under age 65. In many patients, the predominant pathology includes neuronal cytoplasmic or intranuclear inclusions of ubiquitinated TAR DNA binding protein 43 (FTLD‐TDP). Recently, a genome‐wide association study identified the first FTLD‐TDP genetic risk factor, in which variants in and around the TMEM106B gene (top SNP rs1990622) were significantly associated with FTLD‐TDP risk. Intriguingly, the most significant association was in FTLD‐TDP patients carrying progranulin (GRN) mutations. Here, we investigated to what extent the coding variant, rs3173615 (p.T185S) in linkage disequilibrium with rs1990622, affects progranulin protein (PGRN) biology and transmembrane protein 106 B (TMEM106B) regulation. First, we confirmed the association of TMEM106B variants with FTLD‐TDP in a new cohort of GRN mutation carriers. We next generated and characterized a TMEM106B‐specific antibody for investigation of this protein. Enzyme‐linked immunoassay analysis of progranulin protein levels showed similar effects upon T185 and S185 TMEM106B over‐expression. However, over‐expression of T185 consistently led to higher TMEM106B protein levels than S185. Cycloheximide treatment experiments revealed that S185 degrades faster than T185 TMEM106B, potentially due to differences in N‐glycosylation at residue N183. Together, our results provide a potential mechanism by which TMEM106B variants lead to differences in FTLD‐TDP risk.

     

Revisiting Ross and Sims (1971): toward a molecular phylogeny of the Biddulphiaceae and Eupodiscaceae (Bacillariophyceae)

The ocellate and pseudocellate diatoms in the Eupodiscaceae and Biddulphiaceae (respectively) are common inhabitants of the marine littoral (and plankton zone) with a rich fossil history making them important components of marine stratigraphic studies and good candidates for molecular dating work. These diatoms are important for un‐derstanding the phylogeny of the diatoms as a whole, as molecular phylogenies have blurred the traditional distinction between the pennate and multipolar non‐pennate diatoms. However, the convoluted taxonomic history of these groups has the potential to disrupt both stratigraphic and molecular dating studies. Although efforts have been made to examine frustule morphology of several ocellate and pseudocellate diatoms and develop a morphological scheme to define genera, very little work has been done to determine how these groups are interrelated. In this study, we use nuclear and chloroplast molecular markers to construct a phylogeny of a diverse sampling of Eupodiscaceae and Biddulphiaceae taxa. The ocellus‐bearing taxa (Eupodiscaceae) are monophyletic, and thus the ocellus may be a useful character in delimiting the Eupodiscaceae, the Biddulphiaceae are polyphyletic and scattered across a number of lineages of multipolar non‐pennate diatoms. Hypothesis testing aimed at assessing the likeliness of several morphology based hypotheses against the molecular data highlights uncertainty in both types of data. We present evidence that there are monophyletic genera within both the Biddulphiaceae and Eupodiscaceae, and recommend the taxa within the Odontella mobilensis/sinensis/regia clade be transferred to a new genus: Trieres Ashworth & Theriot.     

Variations and trends of birch pollen seasons during 15 years (1996–2010) in relation to weather conditions in Poznań (western Poland)

Birch (Betula) pollen seasons were examined in relation to meteorological conditions in Poznań (1996–2010). Birch pollen grains were collected using a volumetric spore trap. An alternate biennial cycle of birch pollen season intensity was noticed in Poznań. The main factors influencing birch pollen season intensity were average daily minimum temperatures during the second fortnight of May and the month of June one year before pollination as well as the intensity of the pollen season of the previous year. Most of the pollen grains are recorded during the first week of the season; the number of pollen grains recorded at this time is positively correlated with mean maximum temperature and negatively correlated with daily rainfall. The significant effect of rainfall in reducing the season pollen index was noticed only during weak pollen seasons (season pollen index <?mean). In addition, mean daily maximum temperature during the first two weeks of the birch pollen season markedly influences its duration. No significant trends in duration and intensity of the pollen season were recorded, however, a slight tendency towards early pollination was observed (?0.4 days/year, p?=?0.310).     

Social encounter networks: characterizing Great Britain

A major goal of infectious disease epidemiology is to understand and predict the spread of infections within human populations, with the intention of better informing decisions regarding control and intervention. However, the development of fully mechanistic models of transmission requires a quantitative understanding of social interactions and collective properties of social networks. We performed a cross-sectional study of the social contacts on given days for more than 5000 respondents in England, Scotland and Wales, through postal and online survey methods. The survey was designed to elicit detailed and previously unreported measures of the immediate social network of participants relevant to infection spread. Here, we describe individual-level contact patterns, focusing on the range of heterogeneity observed and discuss the correlations between contact patterns and other socio-demographic factors. We find that the distribution of the number of contacts approximates a power-law distribution, but postulate that total contact time (which has a shorter-tailed distribution) is more epidemiologically relevant. We observe that children, public-sector and healthcare workers have the highest number of total contact hours and are therefore most likely to catch and transmit infectious disease. Our study also quantifies the transitive connections made between an individual''s contacts (or clustering); this is a key structural characteristic of social networks with important implications for disease transmission and control efficacy. Respondents'' networks exhibit high levels of clustering, which varies across social settings and increases with duration, frequency of contact and distance from home. Finally, we discuss the implications of these findings for the transmission and control of pathogens spread through close contact.     

The epidemiology underlying age‐related avian malaria infection in a long‐lived host: the mute swan Cygnus olor

Quantifying the factors that predict parasite outbreak and persistence is a major challenge for both applied and fundamental biology. Key to understanding parasite prevalence and disease outbreaks is determining at what age individuals show signs of infection, and whether or not they recover. Age‐dependent patterns of the infection of a host population by parasites can indicate among‐individual heterogeneities in their susceptibility to, or rate of recovery from, parasite infections. Here, we present a cross‐sectional study of avian malaria in a long‐lived bird species, the mute swan Cygnus olor, examining age‐related patterns of parasite prevalence and modelling patterns of infection and recovery. One‐hundred and fifteen swans, ranging from one to nineteen years old, were screened for infection with Plasmodium, Haemoproteus and Leucocytozoon parasites. Infections with three cytochrome‐b lineages of Haemoproteus were found (pooled prevalence 67%), namely WW1 (26%), which is common in passerine birds, and two new lineages closely related to WW1: MUTSW1 (25%) and MUTSW2 (16%). We found evidence for age‐related infection in one lineage, MUTSW1. Catalytic models examining patterns of infection and recovery in the population suggested that infections in this population were not life‐long – recovery of individuals was included in the best fitting models. These findings support the results of recent studies that suggest hosts can clear infections, although patterns of infection‐related mortality in older birds remain to be studied in more detail.