Classification of gene trees is an important task both in the analysis of multi-locus phylogenetic data, and assessment of the convergence of Markov Chain Monte Carlo (MCMC) analyses used in Bayesian ...phylogenetic tree reconstruction. The logistic regression model is one of the most popular classification models in statistical learning, thanks to its computational speed and interpretability. However, it is not appropriate to directly apply the standard logistic regression model to a set of phylogenetic trees, as the space of phylogenetic trees is non-Euclidean and thus contradicts the standard assumptions on covariates. It is well-known in tropical geometry and phylogenetics that the space of phylogenetic trees is a tropical linear space in terms of the max-plus algebra. Therefore, in this paper, we propose an analogue approach of the logistic regression model in the setting of tropical geometry. Our proposed method outperforms classical logistic regression in terms of Area under the ROC Curve in numerical examples, including with data generated by the multi-species coalescent model. Theoretical properties such as statistical consistency have been proved and generalization error rates have been derived. Finally, our classification algorithm is proposed as an MCMC convergence criterion for Mr Bayes. Unlike the convergence metric used by Mr Bayes which is only dependent on tree topologies, our method is sensitive to branch lengths and therefore provides a more robust metric for convergence. In a test case, it is illustrated that the tropical logistic regression can differentiate between two independently run MCMC chains, even when the standard metric cannot.
PurposeThe authors sought to examine how hegemonic masculinity and sexism functioned in a storied, historic corporation, a test of MAnne's (2017) claim that misogyny is a structural phenomenon rather ...than being about anger and hatred of individual men.Design/methodology/approachThis study was an archaeological excavation of discourse in a well-documented employment relationship. The researchers were informed by feminist poststructuralism and drew on critical discourse analysis of labour arbitration and media from the case of a woman, twice wrongfully dismissed.FindingsThe authors concluded that the employer was the site of hegemonic masculinity, which led to a train conductor being repeatedly targeted and demeaned in a bad faith and discriminatory manner for disrupting the conductor’s employer's patriarchal strictures. The authors found that misogyny shaped the conductors’s experience as a repeated pattern of abuse, a gendered feature of a patriarchal organisation, and a coercive matter of maintaining the conductor’s subordination. The authors also found that the male arbitrator in the conductor’s second dismissal arbitration became complicit in misogyny by penalising the conductor for acts of resistance, giving the employer what the employer wanted, to purge the conductor for violating the patriarchal norms.Originality/valueThe authors traced how a historic corporation demonstrated vulnerability to the resistance of a lone female worker, who faced discriminatory, disturbing and bad faith managerial behaviour in the creation of the conductor’s own meaning and resistant identity. The authors concluded that evidence of the regulation of employee relations, such as the decisions of arbitrators, can reveal the processes and outcomes of work under hegemonic masculinity, sexism and misogyny.
An increase in habitat complexity is thought to decrease visibility and the territory size of visually oriented animals. Hence, the addition of physical structure has been viewed as a useful ...restoration technique to increase the density of territorial species, particularly in stream fishes. However, a decrease in territory size may have a negative effect on the fitness of individual organisms. We attempted to quantify some of the positive and negative effects of increasing habitat structure on the behaviour and growth rate of wild young‐of‐the‐year (YOY) Atlantic salmon. Fish were exposed to one of two habitat treatments in mesh enclosures in Catamaran Brook, New Brunswick: a gravel substrate (low complexity) or a gravel substrate with boulders added (high complexity). Wild‐caught individuals were tagged, weighed and measured before being stocked at densities of 1·m⁻² for 7‐d trials. While fish from high‐complexity treatments benefited from lower rates of aggression, they also had lower foraging rates and smaller territories compared to those in low‐complexity treatments. Specific growth rate, however, did not differ significantly between treatments. While the addition of structure to a habitat may be beneficial at the population level in terms of an increase in population density, our results suggested that individual fish may pay some short‐term costs in these environments. Further research is needed to evaluate the longer term costs and benefits of adding structure to improve the habitat quality for stream salmonids.
Important variation in the shape and strength of density‐dependent growth and mortality is observed across animal populations. Understanding this population variation is critical for predicting ...density‐dependent relationships in natural populations, but comparisons amongst studies are challenging as studies differ in methodologies and in local environmental conditions.
Consequently, it is unclear whether: (a) the shape and strength of density‐dependent growth and mortality are population‐specific; (b) the potential trade‐off between density‐dependent growth and mortality differs amongst populations; and (c) environmental characteristics can be related to population differences in density‐dependent relationships.
To elucidate these uncertainties, we manipulated the density (0.3–7 fish/m2) of young‐of‐the‐year brook trout (Salvelinus fontinalis) simultaneously in three neighbouring populations in a field experiment in Newfoundland, Canada. Within each population, our experiment included both spatial (three sites per stream) and temporal (three consecutive summers) replication.
We detected temporally consistent population variation in the shape of density‐dependent growth (negative linear and negative logarithmic), but not for mortality (positive logarithmic). The strength of density‐dependent growth across populations was reduced in sections with a high percentage of boulder substrate, whereas density‐dependent mortality increased with increasing flow, water temperature and more acidic pH. Neighbouring populations exhibited different mortality‐growth trade‐offs: the ratio of mortality‐to‐growth increased linearly with increasing density at different rates across populations (up to 4‐fold differences), but also increased with increasing temperature.
Our results are some of the first to demonstrate temporally consistent, population‐specific density‐dependent relationships and trade‐offs at small spatial scales that match the magnitude of interspecific variation observed across the globe. Furthermore, key environmental characteristics explain some of these differences in predictable ways. Such population differences merit further attention in models of density dependence and in science‐based management of animal populations.
This field experiment is the first to demonstrate temporally consistent, population‐specific patterns of density‐dependent growth, mortality and their trade‐off at small spatial scales in salmonids. This variation in patterns matches the magnitude of interspecific variation observed across the globe and can be related to key environmental characteristics in predictable ways.
Evolution of laughter from play Grant-Jacob, James A
Communicative & integrative biology,
2024, Letnik:
17, Številka:
1
Journal Article
Recenzirano
Odprti dostop
In this hypothesis, I discuss how laughter from physical play could have evolved to being induced via visual or even verbal stimuli, and serves as a signal to highlight incongruity that could ...potentially pose a threat to survival. I suggest how laughter's induction could have negated the need for physical contact in play, evolving from its use in tickling, to tickle-misses, and to taunting, and I discuss how the application of deep learning neural networks trained on images of spectra of a variety of laughter types from a variety of individuals or even species, could be used to determine such evolutionary pathways via the use of latent space exploration.
Threats to Endangered Species in Canada VENTER, OSCAR; BRODEUR, NATHALIE N; NEMIROFF, LEAH ...
Bioscience,
11/2006, Letnik:
56, Številka:
11
Journal Article
Recenzirano
Odprti dostop
We quantified the threats facing 488 species in Canada, categorized by COSEWIC (Committee on the Status of Endangered Wildlife in Canada) as extinct, extirpated, endangered, threatened, or of special ...concern. Habitat loss is the most prevalent threat (84%), followed by overexploitation (32%), native species interactions (31%), natural causes (27%), pollution (26%), and introduced species (22%). Agriculture (46%) and urbanization (44%) are the most common human activities causing habitat loss and pollution. For extant species, the number of threats per species increases with the level of endangerment. The prevalence of threat types varies among major habitats, with overexploitation being particularly important, and introduced species particularly unimportant, for marine species. Introduced species are a much less important threat in Canada than in the United States, but the causes of endangerment are broadly similar for Canadian and globally endangered species.
The loss of spawning habitat has been identified as a limiting factor to population growth for lake sturgeon, Acipenser fulvescens, the most widely distributed species of the family in North America. ...While local information exists about lake sturgeon spawning habitat, a synthesis of all available data is needed across its range. Our study used meta-analytical techniques to describe the mean and range of critical spawning habitat characteristics based on data from 48 sites across all major watersheds in which lake sturgeon are found. Data were compiled into univariate habitat suitability indices to describe the spawning niche. Results indicate that peak suitability occurred at depth-averaged velocities of 0.6 m·s
−1
, depths of 0.55–0.85 m in small rivers (<100 m
3
·s
−1
annual average discharge) and 0.75–5.25 m in large rivers (>100 m
3
·s
−1
), over cobble substrates (64–256 mm), and that suitable water temperatures decreased with increasing latitude. This study provides a comprehensive review of critical spawning criteria from which future habitat suitability models can be adapted.
In a previous analysis, six major threats to at-risk species in Canada were quantified: habitat loss, introduced species, over-exploitation, pollution, native species interactions, and natural causes ...(O. Venter et al. 2006. Bioscience, 56(11): 903–910). Because of rapid environmental change in Canada and an enhanced understanding of the drivers of species endangerment, we updated the 2005 analysis and tested for changes in threats up until the end of 2018. We also expanded the scope to acknowledge climate change as a seventh major threat to species, given its increasing importance for reshaping biological communities. Using information on the COSEWIC (Committee on the Status of Endangered Wildlife in Canada) website, we scored the threats for each of 814 species. Habitat loss remained the most important anthropogenic threat to Canada’s at-risk species, affecting 82% of species, followed by over-exploitation (47%), introduced species (46%), and pollution (35%). Climate change was the least important threat, affecting only 13% of species. However, report writers used less certain language when talking about climate change compared with other threats, so when we included cases where climate change was listed as a probable or future cause, climate change was the fourth most important anthropogenic threat, affecting some 38% of species. The prevalence of threat categories was broadly similar to those for the United States and IUCN listed species. The taxa most affected by climate change included lichens (77%), birds (63%), marine mammals (60%), and Arctic species of all taxa (79%), whereas vascular plants (23%), marine fishes (24%), arthropods (27%), and non-Arctic species (35%) were least affected. A paired analysis of the 188 species with two or more reports indicated that any mention of climate change as a threat increased from 12% to 50% in 10 years. Other anthropogenic threats that have increased significantly over time in the paired analysis included introduced species, over-exploitation, and pollution. Our analysis suggests that threats are changing rapidly over time, emphasizing the need to monitor future trends of all threats, including climate change.
Lors d’une analyse précédente, six menaces majeures pesant sur des espèces en péril au Canada ont été quantifiées : la perte d’habitat, les espèces introduites, la surexploitation, la pollution, les interactions entre les espèces indigènes et les causes naturelles (O. Venter et al. 2006. Bioscience, 56(11): 903–910). En raison des changements environnementaux rapides au Canada et d’une meilleure compréhension des facteurs qui menacent les espèces, les auteurs ont mis à jour l’analyse qui datait de 2005 et examiné l’évolution des menaces jusqu’à la fin de 2018. Ils ont aussi élargi la portée de l’observation pour considérer les changements climatiques en tant que septième menace majeure pour les espèces, compte tenu de leur importance croissante dans le remodelage des communautés biologiques. À l’aide de l’information tirée du site web du COSEPAC (Comité sur la situation des espèces en péril au Canada), les auteurs ont évalué les menaces pour chacune des 814 espèces. La perte d’habitat demeurait la menace anthropique la plus importante pour les espèces en péril du Canada, touchant 82 % des espèces, suivie de la surexploitation (47 %), des espèces introduites (46 %) et de la pollution (35 %). Les changements climatiques constituaient la menace la moins importante, ne touchant que 13 % des espèces. Toutefois, les auteurs des rapports utilisaient un langage moins affirmé lorsqu’ils traitaient des changements climatiques comparativement à d’autres menaces, ce qui a fait que lorsque les auteurs ont inclus les cas où les changements climatiques étaient répertoriéscommecause probable ou future, ils constituaient la quatrième menace anthropique la plus importante, affectant quelque 38 % des espèces. La prévalence des catégories de menaces était généralement similaire à celle des espèces répertoriées par les États-Unis et l’UICN. Les taxons les plus affectés par les changements climatiques comprenaient les lichens (77 %), les oiseaux (63 %), les mammifères marins (60 %) et les espèces arctiques de tous les taxons (79 %), tandis que les plantes vasculaires (23 %), les poissons marins (24 %), les arthropodes (27 %) et les espèces non arctiques (35 %) étaient les moins affectés. Une analyse par paires des 188 espèces avec deux rapports ou plus indiquait que toute mention des changements climatiques en tant que menace a augmenté de 12 % à 50 % en 10 ans. Les autres menaces anthropiques qui se sont accrues significativement au fil du temps selon l’analyse par paires comprenaient les espèces introduites, la surexploitation et la pollution. L’analyse des auteurs suggère que les menaces changent rapidement au fil du temps, soulignant la nécessité de surveiller les tendances futures de toutes les menaces, y compris les changements climatiques.
Vatican't? Grant, James
Review (Institute of Public Affairs (Australia) : 1997),
10/2018, Letnik:
70, Številka:
3
Journal Article
The failure of the Vatican under Pope Francis to stand up for persecuted Catholics and Catholic beliefs is a grave threat to Catholicism and all Catholics.
The interaction between light and matter during laser machining is particularly challenging to model via analytical approaches. Here, we show the application of a statistical approach that constructs ...a model of the machining process directly from experimental images of the laser machined sample, and hence negating the need for understanding the underlying physical processes. Specifically, we use a neural network to transform a laser spatial intensity profile into an equivalent scanning electron microscope image of the laser-machined target. This approach enables the simulated visualization of the result of laser machining with any laser spatial intensity profile, and hence demonstrates predictive capabilities for laser machining. The trained neural network was found to have encoded functionality that was consistent with the laws of diffraction, hence showing the potential of this approach for discovering physical laws directly from experimental data.
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