Summary Gorillas are humans’ closest living relatives after chimpanzees, and are of comparable importance for the study of human origins and evolution. Here we present the assembly and analysis of a genome sequence for the western lowland gorilla, and compare the whole genomes of all extant great ape genera. We propose a synthesis of genetic and fossil evidence consistent with placing the human-chimpanzee and human-chimpanzee-gorilla speciation events at approximately 6 and 10 million years ago (Mya). In 30% of the genome, gorilla is closer to human or chimpanzee than the latter are to each other; this is rarer around coding genes, indicating pervasive selection throughout great ape evolution, and has functional consequences in gene expression. A comparison of protein coding genes reveals approximately 500 genes showing accelerated evolution on each of the gorilla, human and chimpanzee lineages, and evidence for parallel acceleration, particularly of genes involved in hearing. We also compare the western and eastern gorilla species, estimating an average sequence divergence time 1.75 million years ago, but with evidence for more recent genetic exchange and a population bottleneck in the eastern species. The use of the genome sequence in these and future analyses will promote a deeper understanding of great ape biology and evolution.

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The African Diaspora in the Western Hemisphere represents one of the largest forced migrations in history and had a profound impact on genetic diversity in modern populations. To date, the fine-scale population structure of descendants of the African Diaspora remains largely uncharacterized. Here we present genetic variation from deeply sequenced genomes of 642 individuals from North and South American, Caribbean and West African populations, substantially increasing the lexicon of human genomic variation and suggesting much variation remains to be discovered in African-admixed populations in the Americas. We summarize genetic variation in these populations, quantifying the postcolonial sex-biased European gene flow across multiple regions. Moreover, we refine estimates on the burden of deleterious variants carried across populations and how this varies with African ancestry. Our data are an important resource for empowering disease mapping studies in African-admixed individuals and will facilitate gene discovery for diseases disproportionately affecting individuals of African ancestry.

Mucormycosis is a life-threatening infection caused by Mucorales fungi. Here we sequence 30 fungal genomes, and perform transcriptomics with three representative Rhizopus and Mucor strains and with human airway epithelial cells during fungal invasion, to reveal key host and fungal determinants contributing to pathogenesis. Analysis of the host transcriptional response to Mucorales reveals platelet-derived growth factor receptor B (PDGFRB) signaling as part of a core response to divergent pathogenic fungi; inhibition of PDGFRB reduces Mucorales-induced damage to host cells. The unique presence of CotH invasins in all invasive Mucorales, and the correlation between CotH gene copy number and clinical prevalence, are consistent with an important role for these proteins in mucormycosis pathogenesis. Our work provides insight into the evolution of this medically and economically important group of fungi, and identifies several molecular pathways that might be exploited as potential therapeutic targets.

Physiological measurements in neuroscience experiments often involve complex stimulus paradigms and multiple data channels. Ephus () is an open-source software package designed for general-purpose data acquisition and instrument control. Ephus operates as a collection of modular programs, including an ephys program for standard whole-cell recording with single or multiple electrodes in typical electrophysiological experiments, and a mapper program for synaptic circuit mapping experiments involving laser scanning photostimulation based on glutamate uncaging or channelrhodopsin-2 excitation. Custom user functions allow user-extensibility at multiple levels, including on-line analysis and closed-loop experiments, where experimental parameters can be changed based on recently acquired data, such as during in vivo behavioral experiments. Ephus is compatible with a variety of data acquisition and imaging hardware. This paper describes the main features and modules of Ephus and their use in representative experimental applications.

The pattern of utilization of Colophospermum mopane by elephant was investigated in a semi‐arid savanna, the Venetia‐Limpopo Nature Reserve, South Africa, using an animal‐based approach. C. mopane is a staple food item in the diet of elephant, with most individual trees being utilized lightly (< 10% of biomass removed). Utilization of branch, foliage and main stems accounted for most of the utilization of trees < 4 m high whilst utilization of bark accounted for the majority of utilization of trees > 4 m high. The most preferred height of utilization of branches was < 1 m above ground level, reflecting the short stature of C. mopane in the study area. Elephant selected C. mopane trees < 2 m in height that had been previously utilized by them; specifically trees where the terminal part of the main stem had been previously broken and had been coppiced (hedging). The preferred size range of branches utilized by elephant was 0.946–1.718 cm in diameter; hedged C. mopane trees in the 1–2 m category had, on average, significantly more branches within this size range than non‐hedged trees. This hedging of C. mopane appears to have increased the availability of a preferred food item.

Abstract. Question: What is the long‐term influence of nutrient availability, productivity and soil pH on grassland community organization? Location: Ukulinga research farm, KwaZulu‐Natal, South Africa. Methods: The influence of fertilization on soil pH, nitrogen (N) and phosphorus (P) on variation in plant traits, community composition and species richness were examined in a 50‐year grassland fertilization experiment. Results: Averaged over 30 years, above‐ground net primary production (ANPP) was 337, 428 and 518 g.m‐2 in sites not fertilized, fertilized with N, and fertilized with N plus P respectively. ANPP depended directly on N‐fertilization but not on P‐fertilization or liming, and responded positively to the interaction of N (first limiting nutrient) and P (second limiting nutrient). Short narrow‐leaved grass species —Themeda triandra, Tristachya leucothrix and Setaria nigrirostris— dominated sites of lowest ANPP where N was limiting (unfertilized, P‐fertilized or limed sites). A tall narrow‐leaved species, Eragrostis curvula, dominated sites of intermediate ANPP where P was limiting (N‐fertilized sites). By contrast, a tall broad‐leaved species, Panicum maximum, dominated the most productive sites where neither N nor P were limiting (N‐ and P‐fertilized sites). Certain species responded to liming and type of N‐fertilizer apparently because of their effects on soil pH. N‐fertilization reduced the density of herbaceous dicots (forbs) from 14 (unfertilized) to two (high N, no P, no lime) and five species per m2 (high N, no P, limed). This effect was attributed to increased ANPP and a decrease in soil pH from 4.6 (KCl) in unfertilized sites to 3.49 (high N, no lime) and 4.65 (high N and lime). Soil acidification had no effect on grass species richness but influenced the abundance of certain species. Conclusions: Grassland community organization is determined not only by the influence of N availability, but also by the hierarchical interaction of N and P availability, in part through their compounded effect on ANPP, and by individualistic species responses to soil pH.

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