Multiple ITS Copies Reveal Extensive Hybridization within Rheum (Polygonaceae), a Genus That Has Undergone Rapid Radiation

During adaptive radiation events, characters can arise multiple times due to parallel evolution, but transfer of traits through hybridization provides an alternative explanation for the same character appearing in apparently non-sister lineages. The signature of hybridization can be detected in incongruence between phylogenies derived from different markers, or from the presence of two divergent versions of a nuclear marker such as ITS within one individual.In this study, we cloned and sequenced ITS regions for 30 species of the genus Rheum, and compared them with a cpDNA phylogeny. Seven species contained two divergent copies of ITS that resolved in different clades from one another in each case, indicating hybridization events too recent for concerted evolution to have homogenised the ITS sequences. Hybridization was also indicated in at least two further species via incongruence in their position between ITS and cpDNA phylogenies. None of the ITS sequences present in these nine species matched those detected in any other species, which provides tentative evidence against recent introgression as an explanation. Rheum globulosum, previously indicated by cpDNA to represent an independent origin of decumbent habit, is indicated by ITS to be part of clade of decumbent species, which acquired cpDNA of another clade via hybridization. However decumbent and glasshouse morphology are confirmed to have arisen three and two times, respectively.These findings suggested that hybridization among QTP species of Rheum has been extensive, and that a role of hybridization in diversification of Rheum requires investigation

A revision of the Anolis carolinensis subgroup supports three species in Cuba, including a new cryptic species (Squamata: Anolidae)

Abstract Cuba is the only landmass with more than one species in the Anolis carolinensis subgroup. We test the hypothesis that three rather than two distinct species occur on Cuba, based on substantial prior evidence of paraphyly. To test this hypothesis, we collected phenotypic data from all described species in the subgroup, including eastern and west-central Cuban populations of A. porcatus, and assessed phenotypic diagnosability using uni- and multivariate analyses. We also examined geographic isolation using all available occurrence records for Cuban lineages. Additionally, we conducted ecological niche modeling and niche overlap analyses, considering only Cuban lineages, to test for ecological differentiation. Finally, we reconstructed phylogenetic trees, incorporating all species from the subgroup for the first time. Our results support the recognition of three species in Cuba: A. allisoni and eastern and west-central A. porcatus as two distinct cryptic species, showing minimal phenotypic differentiation but clear geographic isolation, distinct ecological niches, and deep genetic divergence. We restrict the name A. porcatus to west-central Cuba, with Havana as the type locality, and formally describe the eastern Cuban populations as Anolis torresfundorai sp. nov., designating Baracoa, Guantánamo, as the type locality

Multi-Locus Phylogeographic and Population Genetic Analysis of Anolis carolinensis: Historical Demography of a Genomic Model Species

The green anole (Anolis carolinensis) has been widely used as an animal model in physiology and neurobiology but has recently emerged as an important genomic model. The recent sequencing of its genome has shed new light on the evolution of vertebrate genomes and on the process that govern species diversification. Surprisingly, the patterns of genetic diversity within natural populations of this widespread and abundant North American lizard remain relatively unknown. In the present study, we use 10 novel nuclear DNA sequence loci (N = 62 to 152) and one mitochondrial locus (N = 226) to delimit green anole populations and infer their historical demography. We uncovered four evolutionarily distinct and geographically restricted lineages of green anoles using phylogenetics, Bayesian clustering, and genetic distance methods. Molecular dating indicates that these lineages last shared a common ancestor ∼2 million years ago. Summary statistics and analysis of the frequency distributions of DNA polymorphisms strongly suggest range-wide expansions in population size. Using Bayesian Skyline Plots, we inferred the timing of population size expansions, which differ across lineages, and found evidence for a relatively recent and rapid westward expansion of green anoles across the Gulf Coastal Plain during the mid-Pleistocene. One surprising result is that the distribution of genetic diversity is not consistent with a latitudinal shift caused by climatic oscillations as is observed for many co-distributed taxa. This suggests that the most recent Pleistocene glacial cycles had a limited impact on the geographic distribution of the green anole at the northern limits of its range

Acidogenic Potential of “Sugar-Free” Cough Drops

A patient presented with extensive marginal ditching around restorations recently placed during whole-mouth rehabilitation. The patient was not xerostomic and was otherwise normal except for the self-reported excessive use of “sugar-free” cough drops sweetened with sorbitol and Isomalt® (an equimolar mix of glucosyl-mannitol and glucosylsorbitol). This prompted an in vitro investigation to determine whether Streptococcus sobrinus 6715, a cariogenic streptococcus, could grow and produce acid in growth medium containing an aqueous extract of such “sugar-free” cough drops. The results indicate that S. sobrinus 6715 uses Isomalt® and sorbitol extensively, producing terminal culture pH as low as 4.2 when grown on medium with cough drop extract containing these sugars. This pH is sufficient to demineralize dental enamel. Patients should be cautioned against the chronic overuse of “sugar-free” cough drops and other “sugar-free” confections sweetened with a mixture of Isomalt® and sorbitol

The Vulnverability Cube: A Multi-Dimensional Framework for Assessing Relative Vulnerability

The diversity and abundance of information available for vulnerability assessments can present a challenge to decision-makers. Here we propose a framework to aggregate and present socioeconomic and environmental data in a visual vulnerability assessment that will help prioritize management options for communities vulnerable to environmental change. Socioeconomic and environmental data are aggregated into distinct categorical indices across three dimensions and arranged in a cube, so that individual communities can be plotted in a three-dimensional space to assess the type and relative magnitude of the communities’ vulnerabilities based on their position in the cube. We present an example assessment using a subset of the USEPA National Estuary Program (NEP) estuaries: coastal communities vulnerable to the effects of environmental change on ecosystem health and water quality. Using three categorical indices created from a pool of publicly available data (socioeconomic index, land use index, estuary condition index), the estuaries were ranked based on their normalized averaged scores and then plotted along the three axes to form a vulnerability cube. The position of each community within the three-dimensional space communicates both the types of vulnerability endemic to each estuary and allows for the clustering of estuaries with like-vulnerabilities to be classified into typologies. The typologies highlight specific vulnerability descriptions that may be helpful in creating specific management strategies. The data used to create the categorical indices are flexible depending on the goals of the decision makers, as different data should be chosen based on availability or importance to the system. Therefore, the analysis can be tailored to specific types of communities, allowing a data rich process to inform decision-making

Radiating on Oceanic Islands: Patterns and Processes of Speciation in the Land Snail Genus Theba (Risso 1826)

Island radiations have played a major role in shaping our current understanding of allopatric, sympatric and parapatric speciation. However, the fact that species divergence correlates with island size emphasizes the importance of geographic isolation (allopatry) in speciation. Based on molecular and morphological data, we investigated the diversification of the land snail genus Theba on the two Canary Islands of Lanzarote and Fuerteventura. Due to the geological history of both islands, this study system provides ideal conditions to investigate the interplay of biogeography, dispersal ability and differentiation in generating species diversity. Our analyses demonstrated extensive cryptic diversification of Theba on these islands, probably driven mainly by non-adaptive allopatric differentiation and secondary gene flow. In a few cases, we observed a complete absence of gene flow among sympatrically distributed forms suggesting an advanced stage of speciation. On the Jandía peninsula genome scans suggested genotype-environment associations and potentially adaptive diversification of two closely related Theba species to different ecological environments. We found support for the idea that genetic differentiation was enhanced by divergent selection in different environments. The diversification of Theba on both islands is therefore best explained by a mixture of non-adaptive and adaptive speciation, promoted by ecological and geomorphological factors

Harnessing Social Enterprise for Local Public Services

The government’s public service reform policy emphasises the collaboration of local authorities with a network of other agencies in the locality, either through contracts or through partnership arrangements. Strong encouragement is currently being given to the involvement of ‘third sector’ organizations (including social enterprises) in such partnering arrangements. This environment has opened up new opportunities for social enterprises. However, as the DTI has asserted in relation to social enterprise, ‘rhetoric rather than a robust evidence base continues to inform many arguments for its growth and support’ (DTI, 2003a: 49). This paper examines one of the most widespread examples of social enterprise in the provision of public services: ‘new leisure trusts’. It asks whether the combination of entrepreneurial skills and social purpose in social enterprises such as new leisure trusts provides a useful model upon which public service partnerships could be based. Findings show that these social enterprises can work to create synergy through improved input/output ratios, commitment to meeting social objectives and wider stakeholder involvement. However, there are issues of incentivisation and relative autonomy that must be resolved within such partnerships, and more work to be done in some cases to build genuine social inclusion

Development and application of an ELISA for the detection of porcine deltacoronavirus IgG antibodies

Porcine deltacoronavirus (PDCoV), also known as porcine coronavirus HKU15, was first detected in North America in early 2014 and associated with enteric disease in pigs, resulting in an urgent need to further investigate the ecology of this virus. While assays detecting nucleic acids were implemented quickly, assays to detect anti-PDCoV antibodies have not been available. In this study, an indirect anti-PDCoV IgG enzyme-linked immunosorbent assay (ELISA) based on the putative S1 portion of the spike protein was developed and utilized to determine the prevalence of anti-PDCoV IgG in U.S. pigs. The diagnostic sensitivity of the PDCoV ELISA was 91% with a diagnostic specificity of 95%. A total of 968 serum samples were tested including samples with confirmed infection with PDCoV, porcine epidemic diarrhea virus (PEDV), transmissible gastroenteritis virus or porcine respiratory coronavirus. There was no cross-reactivity with any of the other coronaviruses. Among 355 arbitrarily selected serum samples collected in 2014 and originating from 51 farms across 18 U.S. states, anti-PDCoV IgG antibodies were detected in 8.7% of the samples and in 25.5% of the farms whereas anti-PEDV IgG was detected in 22.8% of the samples and in 54.9% of the farms. In addition, anti-PDCoV IgG antibodies were detected in archived samples collected in 2010, perhaps indicating an earlier undetected introduction into the U.S. pig population. Overall, the obtained data suggest that PDCoV seroprevalence in U.S. pigs is lower compared to PEDV and PDCoV may have been introduced to the U.S. prior to PEDV