Accounting for matching uncertainty in two stage capture–recapture experiments using photographic measurements of natural marks

We propose a Bayesian hierarchical modeling approach for estimating the size of a closed population from data obtained by identifying individuals through photographs of natural markings. We assume that noisy measurements of a set of distinctive features are available for each individual present in a photographic catalogue. To estimate the population size from two catalogues obtained during two different sampling occasions, we embed the standard two-stage $M_t$ capture–recapture model for closed population into a multivariate normal data matching model that identifies the common individuals across the catalogues. In addition to estimating the population size while accounting for the matching process uncertainty, this hierarchical modelling approach allows to identify the common individuals by using the information provided by the capture–recapture model. This way, our model also represents a novel and reliable tool able to reduce the amount of effort researchers have to expend in matching individuals. We illustrate and motivate the proposed approach via a real data set of photo-identification of narwhals. Moreover, we compare our method with a set of possible alternative approaches by using both the empirical data set and a simulation study.     

Low levels of global genetic differentiation and population expansion in the deep-sea teleost <Emphasis Type="Italic">Hoplostethus atlanticus</Emphasis> revealed by mitochondrial DNA sequences

The orange roughy Hoplostethus atlanticus is a well-known commercial species with a global distribution. There is no consensus about levels of connectivity among populations despite a range of techniques having been applied. We used cytochrome c oxidase subunit I (COI) and cytochrome b sequences to study genetic connectivity at a global scale. Pairwise Φ_ST analyses revealed a lack of significant differentiation among samples from New Zealand, Australia, Namibia, and Chile. However, low but significant differentiation (Φ_ST = 0.02–0.13, P < 0.05) was found between two Northeast Atlantic sites and all the other sites with COI. AMOVA and the haplotype genealogy confirmed these results. The prevalent lack of genetic differentiation is probably due to active adult dispersal under the stepping-stone model. Demographic analyses suggested the occurrence of two expansion events during the Pleistocene period.     

Eulerian and lagrangian transport time scales of a tidal active coastal basin

In this work the flushing features of a tidal active coastal basin, the Venice lagoon, have been investigated. The water transport time scale (TTS) has been computed by means of both an eulerian and a lagrangian approach. The obtained results have been compared in order to identify the main differences between the two methods.     

Multiple sexual pigments,assortative social pairing,and genetic paternity in the yellow warbler (Setophaga petechia)

In socially monogamous species, extra-pair paternity may increase the reproductive success of highly ornamented males, mediating the evolution of sexual ornaments. However, ornaments may also attract social mates, and a tradeoff between extra-pair paternity (EPP) and within-pair paternity (WPP) may complicate mating strategies. Further, in many socially monogamous species, females are also ornamented, and the relationship between female ornamentation and patterns of EPP has been neglected. We investigated the patterns of genetic paternity with respect to carotenoid- and melanin-based pigmentation in yellow warblers (Setophaga petechia) of both sexes. We asked whether males face tradeoffs between EPP and WPP, how paternity patterns relate to carotenoid- versus melanin-based pigmentation, and whether less EPP occurs in broods when males and females are assortatively paired. Males faced a tradeoff between EPP and WPP. Moreover, non-additive relationships existed between paternity patterns and the two pigment types in both sexes. Males with high melanin coverage but dull carotenoid pigmentation achieved EPP but lost WPP, whereas males with high levels of both pigment types had high WPP but gained little EPP. A parallel pattern occurred in females. Warblers paired assortatively by pigmentation and EPP was less common in broods when the sexes were assortatively paired by carotenoid pigmentation. Results suggest that the most colorful birds obtain high quality social mates and advance reproductive success through WPP, show that correlations can arise between female ornamentation and patterns of EPP, and also uniquely suggest that social pairing patterns may influence extra-pair mating strategies.     

Priority areas for conservation of Old World vultures

The prosperity and well-being of human societies relies on healthy ecosystems and the services they provide. However, the biodiversity crisis is undermining ecosystems services and functions. Vultures are among the most imperiled taxonomic groups on Earth, yet they have a fundamental ecosystem function. These obligate scavengers rapidly consume large amounts of carrion and human waste, a service that may aid in both disease prevention and control of mammalian scavengers, including feral dogs, which in turn threaten humans. We combined information about the distribution of all 15 vulture species found in Europe, Asia, and Africa with their threats and used detailed expert knowledge on threat intensity to prioritize critical areas for conserving vultures in Africa and Eurasia. Threats we identified included poisoning, mortality due to collision with wind energy infrastructures, and other anthropogenic activities related to human land use and influence. Areas important for vulture conservation were concentrated in southern and eastern Africa, South Asia, and the Iberian Peninsula, and over 80% of these areas were unprotected. Some vulture species required larger areas for protection than others. Finally, countries that had the largest share of all identified important priority areas for vulture conservation were those with the largest expenditures related to rabies burden (e.g., India, China, and Myanmar). Vulture populations have declined markedly in most of these countries. Restoring healthy vulture populations through targeted actions in the priority areas we identified may help restore the ecosystem services vultures provide, including sanitation and potentially prevention of diseases, such as rabies, a heavy burden afflicting fragile societies. Our findings may guide stakeholders to prioritize actions where they are needed most in order to achieve international goals for biodiversity conservation and sustainable development.     

Variation in male sailfin molly, preference for female size: does sympatry with sexual parasites, drive preference for smaller conspecifics?

Male sailfin mollies (Poecilia latipinna) are sexually parasitized by gynogenetic Amazon mollies (Poecilia formosa). In areas of sympatry, Amazon mollies are frequently larger than female sailfin mollies. In sympatry, selection may favor males that prefer smaller conspecific mates (avoid mismating with Amazon mollies), or selection may favor males that prefer larger conspecific mates (higher fecundity). To explore this potential species and mate-quality recognition conflict, we examined male preference variation across populations. Males from one sympatric population showed stabilizing preference functions, whereas in another sympatric population, males showed directional preference functions. Variation across sympatric populations may be related to the length of time of co-evolution with Amazon mollies. In the allopatric populations, we found flat preference functions. Variation in male preferences could have important ramifications for the maintenance of Amazon mollies, as well as for the evolution of female size.     

Two-phase SPH modelling of advective diffusion processes

This paper deals with a two-dimensional numerical model based on the smoothed particle hydrodynamics (SPH) technique for the evaluation of the concentration field of pollutants in water. A SPH model is formulated to solve the fickian diffusion equation applied to pollutants with the same density as the water. A lagrangian SPH formalism of the advective diffusion equation is also developed for pollutant-water, taking into account the effects of molecular diffusion and natural advection induced by differences between the fluid densities. These equations are coupled with the fluid mechanics equations. Attention is paid to the numerical aspects involved in the solution procedure and to the optimization of the model parameters. Environmental engineering problems concerning diffusion and natural advection phenomena occur in the presence of a pollutant in still water. Numerical tests referring to a strip and a bubble of contaminant in a water tank with different initial concentration laws have been carried out. The results obtained by the proposed SPH models are compared with other available SPH formulations, showing an overall better agreement with standard analytical solutions in terms of spatial evolution of the concentration values. Capabilities and limits of the proposed SPH models to simulate advective diffusion phenomena for a wide range of density ratios are discussed.     

Temperature niche composition change inside and outside protected areas under climate warming

Conservation of biodiversity relies heavily on protected areas but their role and effectiveness under a warming climate is still debated. We estimated the climate-driven changes in the temperature niche compositions of bird communities inside and outside protected areas in southern Canada. We hypothesized that communities inside protected areas include a higher proportion of cold-dwelling species than communities outside protected areas. We also hypothesized that communities shift to warm-dwelling species more slowly inside protected areas than outside. To study community changes, we used large-scale and long-term (1997–2019) data from the Breeding Bird Survey of Canada. To describe the temperature niche compositions of bird communities, we calculated the community temperature index (CTI) annually for each community inside and outside protected areas. Generally, warm-dwelling species dominated communities with high CTI values. We modeled temporal changes in CTI as a function of protection status with linear mixed-effect models. We also determined which species contributed most to the temporal changes in CTI with a jackknife approach. As anticipated, CTI was lower inside protected areas than outside. However, contrary to our expectation, CTI increased faster over time inside than outside protected areas and warm-dwelling species contributed most to CTI change inside protected areas. These results highlight the ubiquitous impacts of climate warming. Currently, protected areas can aid cold-dwelling species by providing habitat, but as the climate warms, the communities’ temperature compositions inside protected areas quickly begin to resemble those outside protected areas, suggesting that protected areas delay the impacts of climate warming on cold-dwelling species.     

Opportunities and challenges for Common Agricultural Policy reform to support the European Green Deal

The Common Agricultural Policy (CAP) is the European Union's main instrument for agricultural planning, with a new reform approved for 2023–2027. The CAP intends to align with the European Green Deal (EGD), a set of policy initiatives underpinning sustainable development and climate neutrality in the European Union (EU), but several flaws cast doubts about the compatibility of the objectives of these 2 policies. We reviewed recent literature on the potential of CAP environmental objectives for integration with the EGD: protection of biodiversity, climate change mitigation and adaptation, and sustainable management of natural resources. The CAP lacks appropriate planning measures, furthering instead risks to biodiversity and ecosystem services driven by landscape and biotic homogenization. Funding allocation mechanisms are not tailored to mitigate agricultural emissions, decreasing the efficiency of climate mitigation actions. The legislation subsidies farmers making extensive use of synthetic inputs without adequately supporting organic production, hindering the transition toward sustainable practices. We recommend proper control mechanisms be introduced in CAP Strategic Plans from each member state to ensure the EU is set on a sustainable production and consumption path. These include proportional assignment of funds to each CAP objective, quantitative targets to set goals and evidence-based interventions, and relevant indicators to facilitate effective monitoring of environmental performance. Both the CAP and the EGD should maintain ambitious environmental commitments in the face of crisis to avoid further degradation of the natural resources on which production systems stand.     

Port safety and the container revolution: A statistical study on human factor and occupational accidents over the long period

Several factors can affect occupational accident frequency, namely economical factors, technologies used (low automation, discontinuous operating) job design, organization of work/environmental conditions and human factors. In particular, technological advances in industrial activities can give rise to improvement in productivity and in occupational health and safety, but not necessarily simultaneously. The beginning of the container transport dates back to 50 years ago, but while containerization changed everything, from ships and ports to patterns of global trade, its impact on work injuries was not explored at all. The aim of this paper is to investigate the relationship between work organization, job experience, productivity and occupational accidents, from the starting of the container expansion to nowadays, considering Genoa port (Italy), one of the largest of the Mediterranean Sea. In order to minimize possible reporting biases, such as underreporting or reclassification to a lower level of severity, injury statistics are elaborated starting from data collected directly on-site, from internal accident or medical-aid reports. An in-depth statistical analysis on occupational injuries in the years 1980–2006 is carried out, with reference to frequency indexes, mechanism of injury and material causes. The increase of container-ships traffic and, consequently, the sharp change in port infrastructure involved a rapid modification also in the work organization, with particular reference to the number and characteristics of workforce (decrease from 5783 to nearly 1000 employees and increase of low experience workers from 28% to 74%). The striking high percentage increase of young or low experienced workers in handling container (and performing correlated new tasks) caused a remarkable increase of the risk for occupational injuries. In the studied port, we recorded an increase of the frequency index (injuries per hundred thousand hours worked) from 13.0 to 29.7. It results that the increased expansion of shipping container utilization is not connected to a correspondent human factor safety implementation. Main risk factors are pointed out, revealing an increase of accidents due to transport vehicle (+8.3%) and a reduction of accidents caused by substance or materials (?4.5%). These factors show a statistical significant correlation with the new job tasks. Consideration of these findings may enable managerial solutions and workplace organization interventions for the prevention of injuries and safety performance improvement in port activities.