Fear of humans as apex predators has landscape-scale impacts from mountain lions to mice

Apex predators such as large carnivores can have cascading, landscape-scale impacts across wildlife communities, which could result largely from the fear they inspire, although this has yet to be experimentally demonstrated. Humans have supplanted large carnivores as apex predators in many systems, and similarly pervasive impacts may now result from fear of the human ‘super predator’. We conducted a landscape-scale playback experiment demonstrating that the sound of humans speaking generates a landscape of fear with pervasive effects across wildlife communities. Large carnivores avoided human voices and moved more cautiously when hearing humans, while medium-sized carnivores became more elusive and reduced foraging. Small mammals evidently benefited, increasing habitat use and foraging. Thus, just the sound of a predator can have landscape-scale effects at multiple trophic levels. Our results indicate that many of the globally observed impacts on wildlife attributed to anthropogenic activity may be explained by fear of humans

Hemisystems of small flock generalized quadrangles

In this paper, we describe a complete computer classification of the hemisystems in the two known flock generalized quadrangles of order $(5^2,5)$ and give numerous further examples of hemisystems in all the known flock generalized quadrangles of order $(s^2,s)$ for $s \le 11$. By analysing the computational data, we identify two possible new infinite families of hemisystems in the classical generalized quadrangle $H(3,q^2)$.Comment: slight revisions made following referee's reports, and included raw dat

The relative effects of prey availability, anthropogenic pressure and environmental variables on lion (Panthera leo) site use in Tanzania's Ruaha landscape during the dry season

African lion (Panthera leo) populations have been reduced by almost half in the past two decades, with national parks and game reserves maintaining vital source populations, particularly in East Africa. However, much of the habitats necessary to support lion populations occur in unprotected lands surrounding protected areas. There is an ongoing need for understanding the ecological determinants of lion occurrence in these unprotected habitats, where lions are most vulnerable to extinction. This study evaluated variations in lion site use along a gradient of anthropogenic pressure encompassing the Ruaha National Park, Pawaga‐Idodi Wildlife Management Area (WMA) and unprotected village lands via camera‐trapping. We collected lion occurrence data in the dry seasons of 2014 and 2015, and modelled lion site use as a function of environmental and anthropogenic variables under a Bayesian framework. We recorded 143 lion detections within the national park, 14 in the WMA and no detections in village lands. This result does not imply that lions never use the village lands, but rather that we did not detect them in our surveys during the dry season. Our findings suggest that lion site use was primarily associated with high seasonal wild prey biomass in protected areas. Thus, we infer that human‐induced prey depletion and lion mortality are compromising lion site use of village lands. Seasonal prey movements, and a corresponding concentration inside the park during sampling, could also play an important role in lion site use. These findings reinforce the need to secure large‐bodied prey base to conserve lions, and the importance of protected areas as key refugia for the species

Response of Wheat Fungal Diseases to Elevated Atmospheric CO2 Level

Infection with fungal pathogens on wheat varieties with different levels of resistance was tested at ambient (NC, 390 ppm) and elevated (EC, 750 ppm) atmospheric CO2 levels in the phytotron. EC was found to affect many aspects of the plant-pathogen interaction. Infection with most fungal diseases was usually found to be promoted by elevated CO2 level in susceptible varieties. Powdery mildew, leaf rust and stem rust produced more severe symptoms on plants of susceptible varieties, while resistant varieties were not infected even at EC. The penetration of Fusarium head blight (FHB) into the spike was delayed by EC in Mv Mambo, while it was unaffected in Mv Regiment and stimulated in Mv Emma. EC increased the propagation of FHB in Mv Mambo and Mv Emma. Enhanced resistance to the spread of Fusarium within the plant was only found in Mv Regiment, which has good resistance to penetration but poor resistance to the spread of FHB at NC. FHB infection was more severe at EC in two varieties, while the plants of Mv Regiment, which has the best field resistance at NC, did not exhibit a higher infection level at EC. The above results suggest that breeding for new resistant varieties will remain a useful means of preventing more severe infection in a future with higher atmospheric CO2 levels

Control de cambios / Rastrea los cambios / El camino cambia: Reflexiones sobre un mundo en transformación

“Track changes: Reflecting on a transforming world” was the theme chosen to invite panels, papers, posters and alternative presentations to be part of the 2019 international congress of SIEF that was held in Santiago de Compostela, Galicia (Spain). This introduction includes a description of the content of the congress, the rationale of the choice of plenaries and some reflections about the outcomes of the congress.El lema elegido para presentar paneles, ponencias, posters y presentaciones en formatos alternativos para el congreso internacional 2019 de SIEF -que tuvo lugar en Santiago de Compostela, Galicia (España)- fue “Track changes: Reflecting on a transforming world”. Esta introducción incluye una descripción del contenido del congreso, la idea para la elección de las plenarias y algunas reflexiones sobre los resultados del congreso. &nbsp

Spanning forests and the q-state Potts model in the limit q \to 0

We study the q-state Potts model with nearest-neighbor coupling v=e^{\beta J}-1 in the limit q,v \to 0 with the ratio w = v/q held fixed. Combinatorially, this limit gives rise to the generating polynomial of spanning forests; physically, it provides information about the Potts-model phase diagram in the neighborhood of (q,v) = (0,0). We have studied this model on the square and triangular lattices, using a transfer-matrix approach at both real and complex values of w. For both lattices, we have computed the symbolic transfer matrices for cylindrical strips of widths 2 \le L \le 10, as well as the limiting curves of partition-function zeros in the complex w-plane. For real w, we find two distinct phases separated by a transition point w=w_0, where w_0 = -1/4 (resp. w_0 = -0.1753 \pm 0.0002) for the square (resp. triangular) lattice. For w > w_0 we find a non-critical disordered phase, while for w < w_0 our results are compatible with a massless Berker-Kadanoff phase with conformal charge c = -2 and leading thermal scaling dimension x_{T,1} = 2 (marginal operator). At w = w_0 we find a "first-order critical point": the first derivative of the free energy is discontinuous at w_0, while the correlation length diverges as w \downarrow w_0 (and is infinite at w = w_0). The critical behavior at w = w_0 seems to be the same for both lattices and it differs from that of the Berker-Kadanoff phase: our results suggest that the conformal charge is c = -1, the leading thermal scaling dimension is x_{T,1} = 0, and the critical exponents are \nu = 1/d = 1/2 and \alpha = 1.Comment: 131 pages (LaTeX2e). Includes tex file, three sty files, and 65 Postscript figures. Also included are Mathematica files forests_sq_2-9P.m and forests_tri_2-9P.m. Final journal versio

Evolutionary characterization of lung adenocarcinoma morphology in TRACERx

Lung adenocarcinomas (LUADs) display a broad histological spectrum from low-grade lepidic tumors through to mid-grade acinar and papillary and high-grade solid, cribriform and micropapillary tumors. How morphology reflects tumor evolution and disease progression is poorly understood. Whole-exome sequencing data generated from 805 primary tumor regions and 121 paired metastatic samples across 248 LUADs from the TRACERx 421 cohort, together with RNA-sequencing data from 463 primary tumor regions, were integrated with detailed whole-tumor and regional histopathological analysis. Tumors with predominantly high-grade patterns showed increased chromosomal complexity, with higher burden of loss of heterozygosity and subclonal somatic copy number alterations. Individual regions in predominantly high-grade pattern tumors exhibited higher proliferation and lower clonal diversity, potentially reflecting large recent subclonal expansions. Co-occurrence of truncal loss of chromosomes 3p and 3q was enriched in predominantly low-/mid-grade tumors, while purely undifferentiated solid-pattern tumors had a higher frequency of truncal arm or focal 3q gains and SMARCA4 gene alterations compared with mixed-pattern tumors with a solid component, suggesting distinct evolutionary trajectories. Clonal evolution analysis revealed that tumors tend to evolve toward higher-grade patterns. The presence of micropapillary pattern and ‘tumor spread through air spaces’ were associated with intrathoracic recurrence, in contrast to the presence of solid/cribriform patterns, necrosis and preoperative circulating tumor DNA detection, which were associated with extra-thoracic recurrence. These data provide insights into the relationship between LUAD morphology, the underlying evolutionary genomic landscape, and clinical and anatomical relapse risk

The artificial intelligence-based model ANORAK improves histopathological grading of lung adenocarcinoma

The introduction of the International Association for the Study of Lung Cancer grading system has furthered interest in histopathological grading for risk stratification in lung adenocarcinoma. Complex morphology and high intratumoral heterogeneity present challenges to pathologists, prompting the development of artificial intelligence (AI) methods. Here we developed ANORAK (pyrAmid pooliNg crOss stReam Attention networK), encoding multiresolution inputs with an attention mechanism, to delineate growth patterns from hematoxylin and eosin-stained slides. In 1,372 lung adenocarcinomas across four independent cohorts, AI-based grading was prognostic of disease-free survival, and further assisted pathologists by consistently improving prognostication in stage I tumors. Tumors with discrepant patterns between AI and pathologists had notably higher intratumoral heterogeneity. Furthermore, ANORAK facilitates the morphological and spatial assessment of the acinar pattern, capturing acinus variations with pattern transition. Collectively, our AI method enabled the precision quantification and morphology investigation of growth patterns, reflecting intratumoral histological transitions in lung adenocarcinoma

The evolution of lung cancer and impact of subclonal selection in TRACERx

Lung cancer is the leading cause of cancer-associated mortality worldwide1. Here we analysed 1,644 tumour regions sampled at surgery or during follow-up from the first 421 patients with non-small cell lung cancer prospectively enrolled into the TRACERx study. This project aims to decipher lung cancer evolution and address the primary study endpoint: determining the relationship between intratumour heterogeneity and clinical outcome. In lung adenocarcinoma, mutations in 22 out of 40 common cancer genes were under significant subclonal selection, including classical tumour initiators such as TP53 and KRAS. We defined evolutionary dependencies between drivers, mutational processes and whole genome doubling (WGD) events. Despite patients having a history of smoking, 8% of lung adenocarcinomas lacked evidence of tobacco-induced mutagenesis. These tumours also had similar detection rates for EGFR mutations and for RET, ROS1, ALK and MET oncogenic isoforms compared with tumours in never-smokers, which suggests that they have a similar aetiology and pathogenesis. Large subclonal expansions were associated with positive subclonal selection. Patients with tumours harbouring recent subclonal expansions, on the terminus of a phylogenetic branch, had significantly shorter disease-free survival. Subclonal WGD was detected in 19% of tumours, and 10% of tumours harboured multiple subclonal WGDs in parallel. Subclonal, but not truncal, WGD was associated with shorter disease-free survival. Copy number heterogeneity was associated with extrathoracic relapse within 1 year after surgery. These data demonstrate the importance of clonal expansion, WGD and copy number instability in determining the timing and patterns of relapse in non-small cell lung cancer and provide a comprehensive clinical cancer evolutionary data resource