The curse of the uncultured fungus

The international DNA sequence databases abound in fungal sequences not annotated beyond the kingdom level, typically bearing names such as "uncultured fungus". These sequences beget lowresolution mycological results and invite further deposition of similarly poorly annotated entries. What do these sequences represent? This study uses a 767,918-sequence corpus of public full-length that represent truly unidentifiable fungal taxa - and what proportion of them that would have deposition. Our results suggest that more than 70% of these sequences would have been trivial to identify to at least the order/family level at the time of sequence deposition, hinting that factors other than poor availability of relevant reference sequences explain the low-resolution names. We speculate that researchers' perceived lack of time and lack of insight into the ramifications of this problem are the main explanations for the low-resolution names. We were surprised to find that more than a fifth of these sequences seem to have been deposited by mycologists rather than researchers unfamiliar with the consequences of poorly annotated fungal sequences in molecular repositories. The proportion of these needlessly poorly annotated sequences does not decline over time, suggesting that this problem must not be left unchecked

Decreased soil moisture due to warming drives phylogenetic diversity and community transitions in the tundra

Global warming leads to drastic changes in the diversity and structure of Arctic plant communities. Studies of functional diversity within the Arctic tundra biome have improved our understanding of plant responses to warming. However, these studies still show substantial unexplained variation in diversity responses. Complementary to functional diversity, phylogenetic diversity has been useful in climate change studies, but has so far been understudied in the Arctic. Here, we use a 25 year warming experiment to disentangle community responses in Arctic plant phylogenetic β diversity across a soil moisture gradient. We found that responses varied over the soil moisture gradient, where meadow communities with intermediate to high soil moisture had a higher magnitude of response. Warming had a negative effect on soil moisture levels in all meadow communities, however meadows with intermediate moisture levels were more sensitive. In these communities, soil moisture loss was associated with earlier snowmelt, resulting in community turnover towards a more heath-like community. This process of 'heathification' in the intermediate moisture meadows was driven by the expansion of ericoid and Betula shrubs. In contrast, under a more consistent water supply Salix shrub abundance increased in wet meadows. Due to its lower stature, palatability and decomposability, the increase in heath relative to meadow vegetation can have several large scale effects on the local food web as well as climate. Our study highlights the importance of the hydrological cycle as a driver of vegetation turnover in response to Arctic climate change. The observed patterns in phylogenetic β diversity were often driven by contrasting responses of species of the same functional growth form, and could thus provide important complementary information. Thus, phylogenetic diversity is an important tool in disentangling tundra response to environmental change.This study was supported by The Swedish Research Council FORMAS (No. 942-2015-1382 to RGB and 2016-01187 to MPB), The Swedish Research Council (No. 621-2014-5315 to RGB and No. 2015-04857 to AA), the European Union's Horizon 2020 research and innovation programme under the Marie Skłodowska-Curie grant agreement (No: 657627 to MPB), BECC—Biodiversity and Ecosystem services in a Changing Climate, the Swedish Foundation for Strategic Research (AA), the Royal Botanic Gardens, Kew (AA), Qatar Petroleum (JMA), and Carl Tryggers Stiftelse för Vetenskaplig Forskning (JMA and MPB)

The Elbow-EpiTrainer : A method of delivering graded resistance to the extensor carpi radialis brevis. Effectiveness of a prototype device in a healthy population

This document is the Accepted Manuscript version of the following article: Navsaria R, Ryder DM, Lewis JS, et al, 'The Elbow-EpiTrainer: a method of delivering graded resistance to the extensor carpi radialis brevi:. Effectiveness of a prototype device in a healthy population', British Journal of Sports Medicine, Vol. 49(5):318-322, March 2015, available online at: http://bjsm.bmj.com/content/49/5/318. Published by the BMJ Publishing Group Limited.Background: Tennis elbow or lateral epicondylopathy (LE) is experienced as the lateral elbow has a reported prevalence of 1.3%, with symptoms lasting up to 18 months. LE is most commonly attributed to tendinopathy involving the extensor carpi radialis brevis (ECRB) tendon. The aim of tendinopathy management is to alleviate symptoms and restore function that initially involves relative rest followed by progressive therapeutic exercise. Objective: To assess the effectiveness of two prototype exercises using commonly available clinical equipment to progressively increase resistance and activity of the ECRB. Method: Eighteen healthy participants undertook two exercise progressions. Surface electromyography was used to record ECRB activity during the two progressions, involving eccentric exercises of the wrist extensors and elbow pronation exercises using a prototype device. The two progressions were assessed for their linearity of progression using repeated ANOVA and linear regression analysis. Five participants repeated the study to assess reliability. Results: The exercise progressions led to an increase in ECRB electromyographic (EMG) activity (p0.7) between the first and second tests for five participants. Conclusions: Manipulation of resistance and leverage with the prototype exercises was effective in creating significant increases of ECRB normalised EMG activity in a linear manner that may, with future research, become useful to clinicians treating LE. In addition, between trial reliability for the device to generate a consistent load was acceptable.Peer reviewe

Data from: SpeciesGeoCoder: fast categorization of species occurrences for analyses of biodiversity, biogeography, ecology and evolution

Understanding the patterns and processes underlying the uneven distribution of biodiversity across space constitutes a major scientific challenge in systematic biology and biogeography, which largely relies on effectively mapping and making sense of rapidly increasing species occurrence data. There is thus an urgent need for making the process of coding species into spatial units faster, automated, transparent, and reproducible. Here we present SpeciesGeoCoder, an open-source software package written in Python and R, that allows for easy coding of species into user-defined operational units. These units may be of any size and be purely spatial (i.e., polygons) such as countries and states, conservation areas, biomes, islands, biodiversity hotspots, and areas of endemism, but may also include elevation ranges. This flexibility allows scoring species into complex categories, such as those encountered in topographically and ecologically heterogeneous landscapes. In addition, SpeciesGeoCoder can be used to facilitate sorting and cleaning of occurrence data obtained from online databases, and for testing the impact of incorrect identification of specimens on the spatial coding of species. The various outputs of SpeciesGeoCoder include quantitative biodiversity statistics, global and local distribution maps, and files that can be used directly in many phylogeny-based applications for ancestral range reconstruction, investigations of biome evolution, and other comparative methods. Our simulations indicate that even datasets containing hundreds of millions of records can be analyzed in relatively short time using a standard computer. We exemplify the use of SpeciesGeoCoder by inferring the historical dispersal of birds across the Isthmus of Panama, showing that lowland species crossed the Isthmus about twice as frequently as montane species with a marked increase in the number of dispersals during the last 10 million years

An engine for global plant diversity: highest evolutionary turnover and emigration in the American tropics

Understanding the processes that have generated the latitudinal biodiversity gradient and the continental differences in tropical biodiversity remains a major goal of evolutionary biology. Here we estimate the timing and direction of range shifts of extant flowering plants (angiosperms) between tropical and non-tropical zones, and into and out of the major tropical regions of the world. We then calculate rates of speciation and extinction taking into account incomplete taxonomic sampling. We use a recently published fossil calibrated phylogeny and apply novel bioinformatic tools to code species into user-defined polygons. We reconstruct biogeographic history using stochastic character mapping to compute relative numbers of range shifts in proportion to the number of available lineages through time. Our results, based on the analysis of c. 22,600 species and c. 20 million geo-referenced occurrence records, show no significant differences between the speciation and extinction of tropical and non-tropical angiosperms. This suggests that at least in plants, the latitudinal biodiversity gradient primarily derives from other factors than differential rates of diversification. In contrast, the outstanding species richness found today in the American tropics (the Neotropics), as compared to tropical Africa and tropical Asia, is associated with significantly higher speciation and extinction rates. This suggests an exceedingly rapid evolutionary turnover, i.e., Neotropical species being formed and replaced by one another at unparalleled rates. In addition, tropical America stands out from other continents by having “pumped out” more species than it received through most of the last 66 million years. These results imply that the Neotropics have acted as an engine for global plant diversity

SpeciesGeoCoder: fast categorization of species occurrences for analyses of biodiversity, biogeography, ecology, and evolution

Understanding the patterns and processes underlying the uneven distribution of biodiversity across space constitutes a major scientific challenge in systematic biology and biogeography, which largely relies on effectively mapping and making sense of rapidly increasing species occurrence data. There is thus an urgent need for making the process of coding species into spatial units faster, automated, transparent, and reproducible. Here we present SpeciesGeoCoder, an open-source software package written in Python and R, that allows for easy coding of species into user-defined operational units. These units may be of any size and be purely spatial (i.e., polygons) such as countries and states, conservation areas, biomes, islands, biodiversity hotspots, and areas of endemism, but may also include elevation ranges. This flexibility allows scoring species into complex categories, such as those encountered in topographically and ecologically heterogeneous landscapes. In addition, SpeciesGeoCoder can be used to facilitate sorting and cleaning of occurrence data obtained from online databases, and for testing the impact of incorrect identification of specimens on the spatial coding of species. The various outputs of SpeciesGeoCoder include quantitative biodiversity statistics, global and local distribution maps, and files that can be used directly in many phylogeny-based applications for ancestral range reconstruction, investigations of biome evolution, and other comparative methods. Our simulations indicate that even datasets containing hundreds of millions of records can be analyzed in relatively short time using a standard computer. We exemplify the use of SpeciesGeoCoder by inferring the historical dispersal of birds across the Isthmus of Panama, showing that lowland species crossed the Isthmus about twice as frequently as montane species with a marked increase in the number of dispersals during the last 10 million years662SI145151FUNDAÇÃO DE AMPARO À PESQUISA DO ESTADO DE SÃO PAULO - FAPESP2009/52161-2; 2013/10262

SpeciesGeoCoder

Github repository for the code presented in this paper. The repository also contains example data for running SpeciesGeoCoder and a wiki with additional information about the program

Supplemental table 1

Supplemental table

SUPERSMART: Self Updating Platform for Estimating Rates of Speciation and Migration, Ages and Relationships of Taxa. Poster

<p>Poster discribing the "SUPERSMART" (Self Updating Platform for Estimating Rates of Speciation and Migration, Ages and Relationships of Taxa) pipeline. </p