BioSimulators: a central registry of simulation engines and services for recommending specific tools

Computational models have great potential to accelerate bioscience, bioengineering, and medicine. However, it remains challenging to reproduce and reuse simulations, in part, because the numerous formats and methods for simulating various subsystems and scales remain siloed by different software tools. For example, each tool must be executed through a distinct interface. To help investigators find and use simulation tools, we developed BioSimulators (https://biosimulators.org), a central registry of the capabilities of simulation tools and consistent Python, command-line and containerized interfaces to each version of each tool. The foundation of BioSimulators is standards, such as CellML, SBML, SED-ML and the COMBINE archive format, and validation tools for simulation projects and simulation tools that ensure these standards are used consistently. To help modelers find tools for particular projects, we have also used the registry to develop recommendation services. We anticipate that BioSimulators will help modelers exchange, reproduce, and combine simulations

Bird tolerance to humans in open tropical ecosystems

AbstractAnimal tolerance towards humans can be a key factor facilitating wildlife–human coexistence, yet traits predicting its direction and magnitude across tropical animals are poorly known. Using 10,249 observations for 842 bird species inhabiting open tropical ecosystems in Africa, South America, and Australia, we find that avian tolerance towards humans was lower (i.e., escape distance was longer) in rural rather than urban populations and in populations exposed to lower human disturbance (measured as human footprint index). In addition, larger species and species with larger clutches and enhanced flight ability are less tolerant to human approaches and escape distances increase when birds were approached during the wet season compared to the dry season and from longer starting distances. Identification of key factors affecting animal tolerance towards humans across large spatial and taxonomic scales may help us to better understand and predict the patterns of species distributions in the Anthropocene.</jats:p

Vocal behaviour of Orange River Francolin Scleroptila levaillantoides based on visual and sound-playback surveys

Fieldwork to study the vocal behaviour of Orange River Francolin Scleroptilia levaillantoides was conducted on a farm in the Heidelberg district, Gauteng province, South Africa, during August 2009 to March 2011. Orange River Francolins possess a basic repertoire of seven calls and one mechanical sound. From 83 francolins tested with playback calls only 33 (39.7%) responded with call backs over the course of the study period. This low response rate in the population is ascribed to habituation because most of the coveys were tested repeatedly on a weekly basis. From a management point of view, call backs can be used to locate coveys in the grass that could then be approached, flushed and counted. Alternatively, it is possible to locate coveys with interactive sound equipment and then multiply the number of call-back localities with an average covey size (about two to three francolins) to determine the size of the population. A &#8216;ke-ri ke-chi&#8217; playback call enticed three different calls from Orange River Francolins that can be used for management purposes, including the &#8216;ke-ri ke-chi&#8217;, cacophony and female calls. These three calls can be used to locate Orange River Francolins, determine dispersion, habitat preferences, breeding cycle and to identify subadults, males and females.OSTRICH 2012, 83(3): 147&#8211;15

Coalition formation, mate selection and pairing behaviour of the Crested Francolin

Transect field observations were conducted on the behaviour of Crested Francolin Dendroperdix sephaena to describe male coalitions in the Borakalalo National Park, North West province, South Africa during May, August, October and December 2008, and again in July 2009. Crested Francolin form male coalitions following the breeding season in May. Young males leave their natal coveys and join old males in these coalitions, which are not based on kinship and consist of up to nine members. These coalitions are joined by a young female from June to October, followed by the breeding season when pairs replace coalitions. The coalition is a prelude to successful mating. The single female calls in the coalition, which triggers a cacophony, and her presence often erupts in physical conflicts between males. This cacophony is interpreted as signal jamming where males prevent one another from forming a duet with the female, clearly showing competition between them for winning over the female for mating. A well-synchronised duet forms the basis of pair formation. Old females are not particularly selected for pairing. The coalition is also a surrogate covey for young males because it optimises predator surveillance. The pair bond also optimises predator surveillance for each other throughout the year

Purpose of Crested Francolin Ortygornis sephaena male collective calls at dusk based on livestream audio censusing

No Abstract

Roosting requirements of Helmeted Guineafowl Numida meleagris on Highveld grain and livestock farms with alien tree groves, Gauteng province, South Africa

This study describes the relationship between Helmeted Guineafowl Numida meleagris and invasive alien trees on livestock and maize farms south-east of Johannesburg, Gauteng province, South Africa. The dependence of the birds on alien trees affects strategies for the removal of these trees. During June to December 2014, Helmeted Guineafowl were recorded weekly on maps along a 42 km transect. Since Helmeted Guineafowl live in cohesive social groups of 15–20 birds, they roost communally in one or two trees during winter rather than spreading across an entire tree grove. The distribution of alien trees across the landscape in patches has enabled Helmeted Guineafowl flocks to reach new feeding patches near to roosting trees, as old feeding patches are depleted. One Helmeted Guineafowl flock of 15–20 birds requires ~0.09 ha covered with mature alien trees for roosting. Suggestions are presented relating to the reduction of alien trees in compliance with the Conservation of Agricultural Resources Act 43 of 1983 and conservation of Helmeted Guineafowl.Keywords: alien trees, communal roosting, farmland, Highveld, Numida meleagri

Age classes of developing Red-necked Spurfowl Pternistis afer based on plumage, morphology and behaviour

This paper describes the plumage and morphology development of 11 age classes of Red-necked Spurfowl Pternistis afer to assist with field observations. Sixteen spurfowl were marked with coloured leg rings in the Cannon Rocks Holiday Resort, Eastern Cape, South Africa during March 2006 and observed daily until June 2008 to describe plumage and non-plumage morphological changes. The age classes include natal chicks, six discernible juvenile phases, post-juvenile phase, near-adult phase, non-territorial and territorial males. Red-necked Spurfowl only attain the adult plumage phase at about 240 d. However, if the development of the bare red throat and spurs are excluded, this near-adult plumage stage is attained at about 180 d. Territorial male Red-necked Spurfowl have long spurs similar to other Pternistis spp. The cryptic downy pattern of chicks assist the birds to blend in with their habitat. However, the plumage of juveniles is simply a transitional phase between the cryptic plumage of downy chicks and the less cryptic plumage of adult spurfowls.Keywords: age classes, camouflage, morphology, plumage development, Pternistis afer, Red-necked Spurfow

Bare-throated spurfowl (Pternistis spp.) males across Africa impress females with bright throat colours during courtship

The role of bare body parts in sexual signalling in birds has received relatively little attention. I describe how the bare-throated spurfowl males saturate the colours of their throats to attract females. Of the 23 Afrotropical spurfowl species, the bare-throated subgroup includes Yellow-necked Spurfowl (Pternistis leucosceptus), Red-necked Spurfowl (P. afer), Grey-breasted Spurfowl (P. rufopictus) and Swainson's Spurfowl (P. swainsonii). The rest of the species include fully feathered throated spurfowls. Throat colour intensity of bare throats was scored using an extensive online digital photographic archive encompassing the four species across the year's seasons. Each throat (n ​= ​836) was assigned to one of four colour-intensity categories to explore the relationship between colour intensities, breeding cycles, and environmental variation. Except for Swainson's Spurfowl male saturation of throat colours correlated with monthly rainfall, which peaks one or two months before egg laying. Swainson's Spurfowl peaks during egg laying. Yellow-necked Spurfowl has the largest bare throat. Bare-throated spurfowl males perform an elevated courtship display posture above the female to feature their throat colour. No such displays occur in feather-throated spurfowl. Males with low throat colour saturation harbour more ectoparasites on their bare throats than birds with saturated throats. Male Red-necked Spurfowls have significantly larger bare throats than females. The primary function of bare throats probably assists in thermoregulation, particularly in arid regions. The bare throat may have evolved a secondary role in mating. Yellow-necked, Red-necked, and Grey-breasted Spurfowls use their saturated throat colours as ornaments to court females during the breeding season. Unobtrusive female throat colours (unsaturated) may discourage male interlopers and predation during egg laying. Saturation appears to be carotenoid-food based. The different colours among the bare-throated species may serve as prezygotic mechanisms that inhibit cross-breeding and explain why females also have coloured throats

Orange River Francolins (Scleroptila levaillantoides) persist in fragmented Highveld farming landscapes, South Africa

Abstract Background How do Orange River Francolins (Scleroptila levaillantoides) adapt to an intensive farming landscape with grass (grazing) camps and crop cultivation? To answer this question, a study was carried out in south-east of Johannesburg in South Africa to clarify the interaction of francolins with a landscape consisting of land use mosaics. Methods A transect-road of 45 km was traversed weekly during November 2015–October 2016 through flat maize (Zea mays) and cattle (Bos primigenius) grazing fields. Francolins were counted in three land use mosaic types along the transect-road (including the road): grass camps on both sides of the road (grass/grass edges); arable fields on both sides (arable/arable edges) and arable land on one side with grass camps on the opposite side of the road (arable/grass edges). Results Francolins used all three mosaic types, but the arable/arable edges were least frequented. Nonetheless, the arable/arable edges played an important part: francolins, including females with chicks, moved along the arable/arable edges, which enabled contact between sub-populations, and the arable/arable edges provided temporary cover (e.g. stubble and maize plants) and ploughed firebreaks to forage (e.g. for bulbs). Conclusion Cultivation of crop within grasslands does not constrain breeding, movement and habitat use by the Orange River Francolin. For conservation purposes it is critical that the fine-scale mosaic of grazing and cultivation areas remain intact

Hierarchical analysis of Swainson’s Spurfowl Pternistis swainsonii habitat use on Highveld maize and livestock farms

This paper explains habitat use by Swainson’s Spurfowl Pternistis swainsonii on maize Zea mays and livestock farms on the Highveld south-east of Johannesburg, South Africa. The purpose is to describe habitat modification methods to manipulate the abundance of Swainson’s Spurfowl on Highveld farms where maize is produced. Field observations were conducted along a 100 km road transect during June 2014–May 2015. A hierarchical habitat analysis with three spatial levels was applied. The location of adult male Swainson’s Spurfowl was used as an indicator of habitat use. Females breed and rear broods in male territories. The micro (2.5-m-radius plot around the birds) and macro (&gt;2.5-m-radius plot) habitats and landscape features were recorded for each sighting. Spurfowl moved within landscapes on a seasonal basis. A micro/macro combination linked with landscape features was a reliable indicator of spurfowl habitat preferences. Micro- and macro-habitats within landscapes can potentially be modified at a single spatial level, or a combination of levels, to manipulate spurfowl abundance on Highveld farms with maize production and livestock.Keywords: hierarchical habitat use, livestock farms, maize fields, Pternistis swainsonii, Swainson’s Spurfow