Challenges and directions in analytical paleobiology.

Over the last 50 years, access to new data and analytical tools has expanded the study of analytical paleobiology, contributing to innovative analyses of biodiversity dynamics over Earth's history. Despite-or even spurred by-this growing availability of resources, analytical paleobiology faces deep-rooted obstacles that stem from the need for more equitable access to data and best practices to guide analyses of the fossil record. Recent progress has been accelerated by a collective push toward more collaborative, interdisciplinary, and open science, especially by early-career researchers. Here, we survey four challenges facing analytical paleobiology from an early-career perspective: (1) accounting for biases when interpreting the fossil record; (2) integrating fossil and modern biodiversity data; (3) building data science skills; and (4) increasing data accessibility and equity. We discuss recent efforts to address each challenge, highlight persisting barriers, and identify tools that have advanced analytical work. Given the inherent linkages between these challenges, we encourage discourse across disciplines to find common solutions. We also affirm the need for systemic changes that reevaluate how we conduct and share paleobiological research.

Glimmers of hope in large carnivore recoveries.

In the face of an accelerating extinction crisis, scientists must draw insights from successful conservation interventions to uncover promising strategies for reversing broader declines. Here, we synthesize cases of recovery from a list of 362 species of large carnivores, ecologically important species that function as terminal consumers in many ecological contexts. Large carnivores represent critical conservation targets that have experienced historical declines as a result of direct exploitation and habitat loss. We examine taxonomic and geographic variation in current extinction risk and recovery indices, identify conservation actions associated with positive outcomes, and reveal anthropogenic threats linked to ongoing declines. We find that fewer than 10% of global large carnivore populations are increasing, and only 12 species (3.3%) have experienced genuine improvement in extinction risk, mostly limited to recoveries among marine mammals. Recovery is associated with species legislation enacted at national and international levels, and with management of direct exploitation. Conversely, ongoing declines are robustly linked to threats that include habitat modification and human conflict. Applying lessons from cases of large carnivore recovery will be crucial for restoring intact ecosystems and maintaining the services they provide to humans.

Fossil dermal denticles reveal the preexploitation baseline of a Caribbean coral reef shark community.

Preexploitation shark baselines and the history of human impact on coral reef-associated shark communities in the Caribbean are tpoorly understood. We recovered shark dermal denticles from mid-Holocene (∼7 ky ago) and modern reef sediments in Bocas del Toro, Caribbean Panama, to reconstruct an empirical shark baseline before major human impact and to quantify how much the modern shark community in the region had shifted from this historical reference point. We found that denticle accumulation rates, a proxy for shark abundance, declined by 71% since the mid-Holocene. All denticle morphotypes, which reflect shark community composition, experienced significant losses, but those morphotypes found on fast-swimming, pelagic sharks (e.g., families Carcharhinidae and Sphyrnidae) declined the most. An analysis of historical records suggested that the steepest decline in shark abundance occurred in the late 20th century, coinciding with the advent of a targeted shark fishery in Panama. Although the disproportionate loss of denticles characterizing pelagic sharks was consistent with overfishing, the large reduction in denticles characterizing demersal species with low commercial value (i.e., the nurse shark Ginglymostoma cirratum) indicated that other stressors could have exacerbated these declines. We demonstrate that the denticle record can reveal changes in shark communities over long ecological timescales, helping to contextualize contemporary abundances and inform shark management and ecology.

Defining variation in pre-human ecosystems can guide conservation: An example from a Caribbean coral reef.

Many Caribbean coral reefs are heavily degraded, yet their pre-human, natural states are often assumed or estimated using space-for-time substitution approaches. Here we use an 11-hectare suite of fossilised mid-Holocene (7.2-5.6 ka) fringing reefs in Caribbean Panama to define natural variation in hard coral community structure before human-impact to provide context to the states of the same reefs today. We collected bulk samples from four trenches dug into the mid-Holocene fossil reef and surficial bulk samples from 2-10 m depths on five adjacent modern reefs extending over 5 km. Analysis of the abundances of coral taxa in fossil bulk samples define the Historical Range of Variation (HRV) in community structure of the reefs. When compared to the community structure of adjacent modern reefs, we find that most coral communities today fall outside the HRV, identifying them as novel ecosystems and corroborating the well-documented transition from acroporid-dominated Caribbean reefs to reefs dominated by stress-tolerant taxa (Porites and Agaricia). We find one modern reef, however, whose community composition remains within the HRV showing that it has not transitioned to a novel state. Reef-matrix cores extracted from this reef reveal that the coral community has remained in this state for over 800 years, suggesting long-term stability and resistance to the region-wide shift to novel states. Without these data to provide historical context, this potentially robust and stable reef would be overlooked since it does not fulfil expectations of what a Caribbean coral reef should look like in the absence of humans. This example illustrates how defining past variation using the fossil record can improve our understanding of modern degradation and guide conservation.

Migration in the Anthropocene: how collective navigation, environmental system and taxonomy shape the vulnerability of migratory species.

Recent increases in human disturbance pose significant threats to migratory species using collective movement strategies. Key threats to migrants may differ depending on behavioural traits (e.g. collective navigation), taxonomy and the environmental system (i.e. freshwater, marine or terrestrial) associated with migration. We quantitatively assess how collective navigation, taxonomic membership and environmental system impact species' vulnerability by (i) evaluating population change in migratory and non-migratory bird, mammal and fish species using the Living Planet Database (LPD), (ii) analysing the role of collective navigation and environmental system on migrant extinction risk using International Union for Conservation of Nature (IUCN) classifications and (iii) compiling literature on geographical range change of migratory species. Likelihood of population decrease differed by taxonomic group: migratory birds were more likely to experience annual declines than non-migrants, while mammals displayed the opposite pattern. Within migratory species in IUCN, we observed that collective navigation and environmental system were important predictors of extinction risk for fishes and birds, but not for mammals, which had overall higher extinction risk than other taxa. We found high phylogenetic relatedness among collectively navigating species, which could have obscured its importance in determining extinction risk. Overall, outputs from these analyses can help guide strategic interventions to conserve the most vulnerable migrations.This article is part of the theme issue 'Collective movement ecology'.

A web-based therapeutic workplace for the treatment of drug addiction and chronic unemployment.

This article describes a Web-based therapeutic workplace intervention designed to promote heroin and cocaine abstinence and train and employ participants as data entry operators. Patients are paid to participate in training and then to perform data entry jobs in a therapeutic workplace business. Salary is linked to abstinence by requiring patients to provide drug-free urine samples to gain access to the workplace. Prior data show that a prototype of the intervention could promote drug abstinence. Preliminary data on the Web-based intervention suggest that it should be able to teach adults with histories of chronic unemployment and drug addiction to become skilled data entry operators in about 3 to 6 months. Early experience in the business provides preliminary evidence that it might become financially successful. The therapeutic workplace intervention may serve as an effective and practical long-term treatment for chronic unemployment and heroin and cocaine addiction.

Computer-based typing and keypad skills raining outcomes of unemployed injection drug users in a therapeutic workplace.

The Therapeutic Workplace is an employment-based treatment for chronic drug misuse and unemployment. As a part of this intervention, participants are taught skills to perform data entry jobs and are paid based on attendance and productivity. In this study, computerized typing and keypad training programs were evaluated in recently detoxified HIV-positive injection drug users (n = 32) enrolled in the Therapeutic Workplace treatment program between October 2000 and September 2001. Results show that trainees can be taught fundamental typing and keypad skills in an average of 51.48 and 1.73h of training, respectively, administered over 17.91 and 12.59 weeks, respectively. Overall, the results demonstrate that adults with long histories of chronic unemployment and drug addiction can reliably acquire typing and keypad skills and do so over relatively short periods of time.

Evaluation of a modified contingency management intervention for consistent attendance in therapeutic workplace participants.

In a therapeutic workplace business, drug abuse patients are hired as data entry operators and paid to perform data entry work contingent upon documented drug abstinence. Reliable attendance has been difficult to maintain despite the opportunity for operators to earn a living wage, 6 h per day, 5 days per week. A within-subject reversal design experiment evaluated a contingency management intervention that allowed for flexibility regarding when operators could arrive to work, yet maintained a contingency for reliable workplace attendance. Results from a within-subject reversal design experiment demonstrated the contingency management intervention to be effective in increasing the frequency of completed work shifts in four of five operators. Repeated measures ANOVA and Tukey's post-hoc tests of grouped data showed that the contingency management intervention significantly (P < 0.05) increased the mean percent of days that operators completed work shifts (5% baseline; 63% contingency management; 7% baseline). This study demonstrates an effective procedure for maintaining attendance in therapeutic workplace participants.

Contingency management of reliable attendance of chronically unemployed substance abusers in a therapeutic workplace.

The Therapeutic Workplace is an effective drug abuse treatment that integrates abstinence reinforcement into a work setting by using a salary that drug abusers earn for work. Drug abuse patients are trained and hired to become data entry operators in a Therapeutic Workplace business. Despite the opportunity to earn a high wage, participants frequently arrive at work late and fail to work complete shifts. In the present study, a contingency management intervention to promote consistent and reliable attendance was evaluated in 4 participants. Participants were not allowed to work on days that they arrived late, and their pay was temporarily reduced each time they arrived late at work or failed to complete a work shift. A within-subject reversal design showed that the intervention increased the frequency with which participants arrived at work on time and completed work shifts.