Data Science in Undergraduate Life Science Education: A Need for Instructor Skills Training.

There is a clear demand for quantitative literacy in the life sciences, necessitating competent instructors in higher education. However, not all instructors are versed in data science skills or research-based teaching practices. We surveyed biological and environmental science instructors (n = 106) about the teaching of data science in higher education, identifying instructor needs and illuminating barriers to instruction. Our results indicate that instructors use, teach, and view data management, analysis, and visualization as important data science skills. Coding, modeling, and reproducibility were less valued by the instructors, although this differed according to institution type and career stage. The greatest barriers were instructor and student background and space in the curriculum. The instructors were most interested in training on how to teach coding and data analysis. Our study provides an important window into how data science is taught in higher education biology programs and how we can best move forward to empower instructors across disciplines.

A question of dissemination: Assessing the practices and implications of research in tropical landscapes.

Current debates in the conservation sciences argue for better integration between research and practice, often citing the importance of the diffusion, dissemination and implementation of scientific knowledge for environmental management and policy. This paper focuses on a relatively well-researched protected area (Madidi National Park) in Bolivia in order to present different interpretations and understandings of the implications and availability of research findings. We draw on findings from quantitative and qualitative methods to determine the extent to which research carried out in the region was disseminated and/or implemented for management actions, and to understand subsequent implications for how local actors perceive the value of research and its role in management and conservation. We discuss the critical consequences of these findings for the future of conservation science and practice in biologically and culturally diverse landscapes, with an explicit call to action for academic institutions to support researchers in developing appropriate dissemination strategies.

Pumas as ecosystem engineers: ungulate carcasses support beetle assemblages in the Greater Yellowstone Ecosystem.

Ecosystem engineers create physical changes in abiotic and biotic material, and through this process control the availability of resources for other species. Predators that abandon large portions of their prey may be ecosystem engineers that create habitat for carrion-dependent invertebrates that utilize carcasses during critical life-history periods. Between 04-May-2016 and 04-Oct-2016, we sampled beetle assemblages at 18 carcasses of prey killed by pumas and matching control sites in the southern Greater Yellowstone Ecosystem, USA, to measure the extent to which beetle families utilized these carcass "habitats". We used generalized linear-mixed models and linear-mixed effect models to examine changes in beetle abundance, species richness, and Simpson's Index of Diversity. We estimated kill rates and carrion production rates for individual pumas to better assess the impact of pumas on invertebrate communities. We collected 24,209 beetles representing 215 species. We identified eight beetle families that had significantly higher abundance at carcasses than control sites. Carcasses had a statistically large to very large effect (determined using Cohen's d) on beetle abundance, richness, and diversity for the initial 8 weeks of sampling. Our research revealed strong effects of an ecosystem engineer on beetle assemblages while highlighting the potential role of apex predators in creating and modifying physical habitats for carrion-dependent species. This suggests that there may be consequences for invertebrate communities where apex predators exist at reduced numbers or have been eradicated. The ecological role of invertebrates is often overlooked, yet they are essential taxa that provide critical ecological services upon which we depend.

Divergent trait and environment relationships among parallel radiations in Pelargonium (Geraniaceae): a role for evolutionary legacy?

Functional traits in closely related lineages are expected to vary similarly along common environmental gradients as a result of shared evolutionary and biogeographic history, or legacy effects, and as a result of biophysical tradeoffs in construction. We test these predictions in Pelargonium, a relatively recent evolutionary radiation. Bayesian phylogenetic mixed effects models assessed, at the subclade level, associations between plant height, leaf area, leaf nitrogen content and leaf mass per area (LMA), and five environmental variables capturing temperature and rainfall gradients across the Greater Cape Floristic Region of South Africa. Trait-trait integration was assessed via pairwise correlations within subclades. Of 20 trait-environment associations, 17 differed among subclades. Signs of regression coefficients diverged for height, leaf area and leaf nitrogen content, but not for LMA. Subclades also differed in trait-trait relationships and these differences were modulated by rainfall seasonality. Leave-one-out cross-validation revealed that whether trait variation was better predicted by environmental predictors or trait-trait integration depended on the clade and trait in question. Legacy signals in trait-environment and trait-trait relationships were apparently lost during the earliest diversification of Pelargonium, but then retained during subsequent subclade evolution. Overall, we demonstrate that global-scale patterns are poor predictors of patterns of trait variation at finer geographic and taxonomic scales.

Intensifying postfire weather and biological invasion drive species loss in a Mediterranean-type biodiversity hotspot.

Prolonged periods of extreme heat or drought in the first year after fire affect the resilience and diversity of fire-dependent ecosystems by inhibiting seed germination or increasing mortality of seedlings and resprouting individuals. This interaction between weather and fire is of growing concern as climate changes, particularly in systems subject to stand-replacing crown fires, such as most Mediterranean-type ecosystems. We examined the longest running set of permanent vegetation plots in the Fynbos of South Africa (44 y), finding a significant decline in the diversity of plots driven by increasingly severe postfire summer weather events (number of consecutive days with high temperatures and no rain) and legacy effects of historical woody alien plant densities 30 y after clearing. Species that resprout after fire and/or have graminoid or herb growth forms were particularly affected by postfire weather, whereas all species were sensitive to invasive plants. Observed differences in the response of functional types to extreme postfire weather could drive major shifts in ecosystem structure and function such as altered fire behavior, hydrology, and carbon storage. An estimated 0.5 °C increase in maximum temperature tolerance of the species sets unique to each survey further suggests selection for species adapted to hotter conditions. Taken together, our results show climate change impacts on biodiversity in the hyperdiverse Cape Floristic Region and demonstrate an important interaction between extreme weather and disturbance by fire that may make flammable ecosystems particularly sensitive to climate change.

Using global sensitivity analysis of demographic models for ecological impact assessment.

Population viability analysis (PVA) is widely used to assess population-level impacts of environmental changes on species. When combined with sensitivity analysis, PVA yields insights into the effects of parameter and model structure uncertainty. This helps researchers prioritize efforts for further data collection so that model improvements are efficient and helps managers prioritize conservation and management actions. Usually, sensitivity is analyzed by varying one input parameter at a time and observing the influence that variation has over model outcomes. This approach does not account for interactions among parameters. Global sensitivity analysis (GSA) overcomes this limitation by varying several model inputs simultaneously. Then, regression techniques allow measuring the importance of input-parameter uncertainties. In many conservation applications, the goal of demographic modeling is to assess how different scenarios of impact or management cause changes in a population. This is challenging because the uncertainty of input-parameter values can be confounded with the effect of impacts and management actions. We developed a GSA method that separates model outcome uncertainty resulting from parameter uncertainty from that resulting from projected ecological impacts or simulated management actions, effectively separating the 2 main questions that sensitivity analysis asks. We applied this method to assess the effects of predicted sea-level rise on Snowy Plover (Charadrius nivosus). A relatively small number of replicate models (approximately 100) resulted in consistent measures of variable importance when not trying to separate the effects of ecological impacts from parameter uncertainty. However, many more replicate models (approximately 500) were required to separate these effects. These differences are important to consider when using demographic models to estimate ecological impacts of management actions.

Population dynamics can be more important than physiological limits for determining range shifts under climate change.

Evidence is accumulating that species' responses to climate changes are best predicted by modelling the interaction of physiological limits, biotic processes and the effects of dispersal-limitation. Using commercially harvested blacklip (Haliotis rubra) and greenlip abalone (Haliotis laevigata) as case studies, we determine the relative importance of accounting for interactions among physiology, metapopulation dynamics and exploitation in predictions of range (geographical occupancy) and abundance (spatially explicit density) under various climate change scenarios. Traditional correlative ecological niche models (ENM) predict that climate change will benefit the commercial exploitation of abalone by promoting increased abundances without any reduction in range size. However, models that account simultaneously for demographic processes and physiological responses to climate-related factors result in future (and present) estimates of area of occupancy (AOO) and abundance that differ from those generated by ENMs alone. Range expansion and population growth are unlikely for blacklip abalone because of important interactions between climate-dependent mortality and metapopulation processes; in contrast, greenlip abalone should increase in abundance despite a contraction in AOO. The strongly non-linear relationship between abalone population size and AOO has important ramifications for the use of ENM predictions that rely on metrics describing change in habitat area as proxies for extinction risk. These results show that predicting species' responses to climate change often require physiological information to understand climatic range determinants, and a metapopulation model that can make full use of this data to more realistically account for processes such as local extirpation, demographic rescue, source-sink dynamics and dispersal-limitation.

How does climate change cause extinction?

Anthropogenic climate change is predicted to be a major cause of species extinctions in the next 100 years. But what will actually cause these extinctions? For example, will it be limited physiological tolerance to high temperatures, changing biotic interactions or other factors? Here, we systematically review the proximate causes of climate-change related extinctions and their empirical support. We find 136 case studies of climatic impacts that are potentially relevant to this topic. However, only seven identified proximate causes of demonstrated local extinctions due to anthropogenic climate change. Among these seven studies, the proximate causes vary widely. Surprisingly, none show a straightforward relationship between local extinction and limited tolerances to high temperature. Instead, many studies implicate species interactions as an important proximate cause, especially decreases in food availability. We find very similar patterns in studies showing decreases in abundance associated with climate change, and in those studies showing impacts of climatic oscillations. Collectively, these results highlight our disturbingly limited knowledge of this crucial issue but also support the idea that changing species interactions are an important cause of documented population declines and extinctions related to climate change. Finally, we briefly outline general research strategies for identifying these proximate causes in future studies.

Biological invasions: a field synopsis, systematic review, and database of the literature.

Species introductions of anthropogenic origins are a major aspect of rapid ecological change globally. Research on biological invasions has generated a large literature on many different aspects of this phenomenon. Here, we describe and categorize some aspects of this literature, to better understand what has been studied and what we know, mapping well-studied areas and important gaps. To do so, we employ the techniques of systematic reviewing widely adopted in other scientific disciplines, to further the use of approaches in reviewing the literature that are as scientific, repeatable, and transparent as those employed in a primary study. We identified 2398 relevant studies in a field synopsis of the biological invasions literature. A majority of these studies (58%) were concerned with hypotheses for causes of biological invasions, while studies on impacts of invasions were the next most common (32% of the publications). We examined 1537 papers in greater detail in a systematic review. Superior competitive abilities of invaders, environmental disturbance, and invaded community species richness were the most common hypotheses examined. Most studies examined only a single hypothesis. Almost half of the papers were field observational studies. Studies of terrestrial invasions dominate the literature, with most of these concerning plant invasions. The focus of the literature overall is uneven, with important gaps in areas of theoretical and practical importance.

Segmentally arranged somatotopy within the face representation of human primary somatosensory cortex.

Though somatotypic representation within the face in human primary somatosensory cortex (S1) to innocuous stimuli is controversial; previous work suggests that painful heat is represented based on an "onion-skin" or segmental pattern on the face. The aim of this study was to determine if face somatotopy for brush stimuli in S1 also follows this segmental representation model. Twelve healthy subjects (nine men: three women) underwent functional magnetic resonance imaging to measure blood oxygen level dependent signals during brush (1 Hz, 15 s) applied to their faces. Separate functional scans were collected for brush stimuli repetitively applied to each of five separate stimulation sites on the right side of the face. These sites were arranged in a vertical, horizontal, and circular manner encompassing the three divisions of the trigeminal nerve. To minimize inter-individual morphological differences in the post-central gyrus across subjects, cortical surface-based registration was implemented before group statistical image analysis. Based on activation foci, somatotopic activation in the post-central gyrus was detected for brush, consistent with the segmental face representation model.

Comparison of evoked vs. spontaneous tics in a patient with trigeminal neuralgia (tic doloureux).

A 53-year old woman with tic doloureaux, affecting her right maxillary division of the trigeminal nerve (V2), could elicit shooting pains by slightly tapping her teeth when off medication. The pains, which she normally rated as > 6/10 on a visual analog scale (VAS), were electric shock-like in nature. She had no other spontaneous or ongoing background pain affecting the region. Based on her ability to elicit these tics, functional magnetic resonance imaging (fMRI) was performed while she produced brief shocks every 2 minutes on cue (evoked pain) over a 20 min period. In addition, she had 1-2 spontaneous shocks manifested between these evoked pains over the course of functional image acquisition. Increased fMRI activation for both evoked and spontaneous tics was observed throughout cortical and subcortical structures commonly observed in experimental pain studies with healthy subjects; including the primary somatosensory cortex, insula, anterior cingulate, and thalamus. Spontaneous tics produced more decrease in signals in a number of regions including the posterior cingulate cortex and amygdala, suggesting that regions known to be involved in expectation/anticipation may have been activated for the evoked, but not spontaneous, tics. In this patient there were large increases in activation observed in the frontal regions, including the anterior cingulate cortex and the basal ganglia. Spontaneous tics showed increased activation in classic aversion circuitry that may contribute to increased levels of anxiety. We believe that this is the first report of functional imaging of brain changes in tic-doloureaux.

Capsaicin-induced thermal hyperalgesia and sensitization in the human trigeminal nociceptive pathway: an fMRI study.

The aim of this study was to differentiate the processing of nociceptive information, matched for pain intensity, from capsaicin-induced hyperalgesic vs. control skin at multiple levels in the trigeminal nociceptive pathway. Using an event-related fMRI approach, 12 male subjects underwent three functional scans beginning 1 h after topical application of capsaicin to a defined location on the maxillary skin, when pain from capsaicin application had completely subsided. Brush and two levels of painful heat (low-Thermal-1 and high-Thermal-2) were applied to the site of capsaicin application and to the mirror image region on the opposite side. Temperatures for each side were set to evoke perceptually matched pain (mean temperatures [capsaicin/control]: Thermal-1=38.4/42.8 degrees C; Thermal-2=44.9/47.8 degrees C). We found differences in activation patterns following stimuli to treated and untreated sides in sensory circuits across all stimulus conditions. Across the trigeminal nociceptive pathway, Thermal-2 stimulation of hyperalgesic skin evoked greater activation in trigeminal ganglion and nucleus, thalamus, and somatosensory cortex than the control side. Thus, trigeminal nociceptive regions showed increased activation in the context of perceptually equal pain levels. Beyond these regions, contrast analyses of capsaicin vs. control skin stimulation indicated significant changes in bilateral dorsolateral prefrontal cortex and amygdala. The involvement of these emotion-related regions suggests that they may be highly sensitive to context, such as prior experience (application of capsaicin) and the specific pain mechanism (hyperalgesic vs. normal skin).