The SABAP2 legacy: A review of the history and use of data generated by a long-running citizen science project

Significance:• The Second Southern African Bird Atlas Project (SABAP2) – initiated in 2007 – is one of the region’s longest-running citizen science programmes and collects spatial and temporal data on birds. • Data from the project are publicly available and used extensively by environmental impact assessment practitioners, conservationists, authors, protected area managers, scientists and the general public.• The project is the template for other established projects that now operate across the continent, collectively now falling under the ‘African Bird Atlas Project’ umbrella.• We show that since the initiation of SABAP2, there has been a three-fold increase in publications, with over 150 papers that can be attributed to SABAP2. • The contribution of citizen scientists to the published scientific domain has been enormous

Large expert-curated database for benchmarking document similarity detection in biomedical literature search

Document recommendation systems for locating relevant literature have mostly relied on methods developed a decade ago. This is largely due to the lack of a large offline gold-standard benchmark of relevant documents that cover a variety of research fields such that newly developed literature search techniques can be compared, improved and translated into practice. To overcome this bottleneck, we have established the RElevant LIterature SearcH consortium consisting of more than 1500 scientists from 84 countries, who have collectively annotated the relevance of over 180 000 PubMed-listed articles with regard to their respective seed (input) article/s. The majority of annotations were contributed by highly experienced, original authors of the seed articles. The collected data cover 76% of all unique PubMed Medical Subject Headings descriptors. No systematic biases were observed across different experience levels, research fields or time spent on annotations. More importantly, annotations of the same document pairs contributed by different scientists were highly concordant. We further show that the three representative baseline methods used to generate recommended articles for evaluation (Okapi Best Matching 25, Term Frequency-Inverse Document Frequency and PubMed Related Articles) had similar overall performances. Additionally, we found that these methods each tend to produce distinct collections of recommended articles, suggesting that a hybrid method may be required to completely capture all relevant articles. The established database server located at https://relishdb.ict.griffith.edu.au is freely available for the downloading of annotation data and the blind testing of new methods. We expect that this benchmark will be useful for stimulating the development of new powerful techniques for title and title/abstract-based search engines for relevant articles in biomedical research.Peer reviewe

Editorial: A message of thanks

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Lesotho annotated bibliography: Section 167A. Birds: annotated species checklist (3rd ed.) by David Ambrose

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Book Review: Biologists in the Age of Totalitarianism: Personal Reminiscences of Ornithologists and Other Naturalists

Book Title: Biologists in the Age of Totalitarianism: Personal Reminiscences of Ornithologists and Other NaturalistsBook Author: Eugeniusz Nowak; English translation edited by Brian Hillcoat2018, Cambridge Scholars Publishing, Lady Stephenson Library, Newcastle upon Tyne, NE6 2PA, United Kingdom. 372 pages, hardcover, photographs.ISBN-13: 978-1-5275-1099-9, ISBN-10: 1-5275-1099-9. Price: £64.99

Editorial: Best student research paper published in Ostrich 2018

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Aspects of the ecology and morphology of the protea seedeater, Crithagra leucopterus, a little-known Fynbos endemic

The protea seedeater, Crithagra leucopterus, is one of six passerine birds endemic to the Fynbos Biome, South Africa. It is the least known of these, and there is very little information on breeding and habitat use. Through nest observations and a bird ringing scheme in the eastern sections of the Fynbos, we provide updated information on habitat use, breeding and population biometrics. We document changes in capture rates for a suite of birds in relation to a fire event and use of burnt and unburnt sites within Blue Hill Nature Reserve, South Africa. Protea seedeaters were recorded nesting in mature Fynbos, but feeding in recently burnt Fynbos on freshly released protea seeds, suggesting the species benefits from smallscale burns that create a landscape of mixed veld ages. Protea seedeaters weighed less and had shorter wings compared to those of the western Fynbos. Further habitat-use and life-history information on protea seedeaters is needed to help guide conservation management plans, especially in the light of changing fire regimes in the Fynbos.Key words: protea canary, fynbos birds, fire ecology

Publication incentives based on journal rankings disadvantage local publications

CITATION: Lee, A. T. K. & Simon, C. A. 2018. Publication incentives based on journal rankings disadvantage local publications. South African Journal of Science, 114(9/10), Art. #a0289, doi:10.17159/sajs.2018/a0289.The original publication is available at http://sajs.co.zaNo abstract available.https://www.sajs.co.za/article/view/5544Publisher's versio

Agulhas long-billed lark (Certhilauda brevirostris) densities, population estimates and habitat association in a transformed landscape

The effects of agricultural landscape transformation and subsequent habitat associations have been little studied for the Agulhas long-billed lark (Certhilauda brevirostris), a regionally threatened species in the Overberg, Western Cape, South Africa. Point count surveys were conducted throughout the Overberg using distance sampling techniques. We calculated bird density and extrapolated this to a population range estimate of between 203 000 and 368 000 individuals. Using generalised linear modelling of habitat variables from the point counts, we found that the birds prefer short vegetation, regardless of habitat type or cover. Broad-scale habitat association patterns were examined using SABAP2 data to determine if reporting rate (a measure of abundance) was correlated with the proportion of natural habitat within each pentad, finding that reporting rates were lower for areas with large patches of natural vegetation and extensive road access. It remains inconclusive whether agricultural practices benefited Agulhas long-billed larks, or whether these practices mimic historical ecological processes, but the population appears secure and even increasing with the status quo.Keywords: agricultural transformation, Alaudidae, distance sampling, endemic species, fynbos, habitat selectio