Pleistocene glaciations caused the latitudinal gradient of within-species genetic diversity.

Intraspecific genetic diversity is a key aspect of biodiversity. Quaternary climatic change and glaciation influenced intraspecific genetic diversity by promoting range shifts and population size change. However, the extent to which glaciation affected genetic diversity on a global scale is not well established. Here we quantify nucleotide diversity, a common metric of intraspecific genetic diversity, in more than 38,000 plant and animal species using georeferenced DNA sequences from millions of samples. Results demonstrate that tropical species contain significantly more intraspecific genetic diversity than nontropical species. To explore potential evolutionary processes that may have contributed to this pattern, we calculated summary statistics that measure population demographic change and detected significant correlations between these statistics and latitude. We find that nontropical species are more likely to deviate from neutral expectations, indicating that they have historically experienced dramatic fluctuations in population size likely associated with Pleistocene glacial cycles. By analyzing the most comprehensive data set to date, our results imply that Quaternary climate perturbations may be more important as a process driving the latitudinal gradient in species richness than previously appreciated.

phylogatR: Phylogeographic data aggregation and repurposing.

Patterns of genetic diversity within species contain information the history of that species, including how they have responded to historical climate change and how easily the organism is able to disperse across its habitat. More than 40,000 phylogeographic and population genetic investigations have been published to date, each collecting genetic data from hundreds of samples. Despite these millions of data points, meta-analyses are challenging because the synthesis of results across hundreds of studies, each using different methods and forms of analysis, is a daunting and time-consuming task. It is more efficient to proceed by repurposing existing data and using automated data analysis. To facilitate data repurposing, we created a database (phylogatR) that aggregates data from different sources and conducts automated multiple sequence alignments and data curation to provide users with nearly ready-to-analyse sets of data for thousands of species. Two types of scientific research will be made easier by phylogatR: large meta-analyses of thousands of species that can address classic questions in evolutionary biology and ecology, and student- or citizen- science based investigations that will introduce a broad range of people to the analysis of genetic data. phylogatR enhances the value of existing data via the creation of software and web-based tools that enable these data to be recycled and reanalysed and increase accessibility to big data for research laboratories and classroom instructors with limited computational expertise and resources.

Analysis of biodiversity data suggests that mammal species are hidden in predictable places.

SignificanceOnly an estimated 1 to 10% of Earth's species have been formally described. This discrepancy between the number of species with a formal taxonomic description and actual number of species (i.e., the Linnean shortfall) hampers research across the biological sciences. To explore whether the Linnean shortfall results from poor taxonomic practice or not enough taxonomic effort, we applied machine-learning techniques to build a predictive model to identify named species that are likely to contain hidden diversity. Results indicate that small-bodied species with large, climatically variable ranges are most likely to contain hidden species. These attributes generally match those identified in the taxonomic literature, indicating that the Linnean shortfall is caused by societal underinvestment in taxonomy rather than poor taxonomic practice.

Design, implementation, and monitoring of HIV service packages for people who inject drugs: An assessment of programs supported by the Global Fund in 46 countries.

BACKGROUND: People who inject drugs (PWID) are at higher risk of acquiring and transmitting HIV, accounting for an estimated 10% of HIV new infections globally. The World Health Organization (WHO) and other international agencies have clearly outlined the comprehensive package of services that should be available for PWID. METHODS: This paper summarizes the data and findings from the PWID service packages assessed in 15 countries across different regions. It also provides data on the design of PWID programs in a further 30 countries that identified PWID as a key population in their national HIV strategic documents. A mixed-method approach was used, including desk reviews, key informant interviews, site observations and group interviews with implementers and PWID focus groups. RESULTS: Design of service packages varied considerably between countries while many matched the WHO Comprehensive Package. Only 85% countries (39/46) included needle-syringe exchange programs (NSEP) and 76% included opioid agonist therapy (OAT). Only 17% countries included overdose management in their package design. Across the 46 countries assessed, the average coverage with defined prevention package was 40% among countries for which coverage figures could be derived. CONCLUSIONS: Despite some examples of client-based, high-quality services in challenging environments, few countries, which rely primarily on external donor support, are reaching the necessary coverage levels across the full range of PWID HIV prevention, testing and care services. Transition from donor to domestic funding to fund this element of the HIV responses in many countries presents a compelling case to prevent PWID from being further left behind.

Advocating for opioid substitution therapy in Central Asia: much still to be done.

Opioid substitution therapy (OST) was first introduced in the formerly-Soviet Central Asian Republics as an HIV prevention intervention for people who inject drugs (PWID) in 2002. Presently, pilot programs function in Kazakhstan and Tajikistan, and Kyrgyzstan has scaled-up from the pilot phase to the operation of over 20 OST sites nation-wide. All three countries have taken steps towards lower-threshold programs, allowing clients to enroll regardless of HIV status, and, in some cases, without documentation of failure to complete other drug treatment programs. However, OST programs remain exclusively funded by international donors, and political and societal opposition to these programs threaten their stability. In order to counter negative campaigns and political attacks on OST, organized advocacy efforts are needed. This commentary explores efforts undertaken by international donor partners supporting advocacy efforts to scale-up OST and assure a sustainable future for programming. It examines both proactive and reactive efforts, and the variety of target audiences that need to be reached to conduct effective advocacy. Ultimately we find that, while a range of tools are available for OST advocacy in the hostile environments of the former Soviet Union, the strengthening of advocacy groups is needed to assure an optimized platform exists for using the evidence and developing relevant materials in the appropriate languages (including, but not limited to, Russian) for both proactive and reactive efforts; and that more robust monitoring is desirable to bring sharper focus to replicable methods.

Training phonological reading in deep alexia: does it improve reading words with low imageability?

The purpose of this study was to examine whether training phonological reading using a bigraph-syllable pairing method (e.g. pa - /pae/) instead of grapheme-phoneme pairing (e.g. p - /p/, a - /ae/) resulted in improved reading of words with low imageability and paragraphs in an individual with deep alexia. In the treatment, Friedman and Lott's bigraph-syllable correspondence (e.g. fa - /fae/) training procedure was adapted and used. The results indicated that the treatment effect generalized to the reading of words with low imageability, which was not reported in most previous studies. Oral reading accuracy and comprehension accuracy of paragraphs also improved. It is suggested that bigraph-syllable correspondence training is effective in improving low imageability word reading, possibly because it can provide more substantial phonemic cues necessary to read words with low imageability (which have limited semantic information associated with them) than the grapheme-phoneme correspondence training method.