Passive Acoustics: A Multifaceted Tool for Marine Mammal Conservation

Marine mammals exploit the efficiency of sound propagation in the marine environment for essential activities like communication and navigation. For this reason, passive acoustics has particularly high potential for marine mammal studies, especially those aimed at population management and conservation. Despite the rapid realization of this potential through a growing number of studies, much crucial information remains unknown or poorly understood. This research attempts to address two key knowledge gaps, using the well-studied bottlenose dolphin (Tursiops truncatus) as a model species, and underwater acoustic recordings collected on four fixed autonomous sensors deployed at multiple locations in Sarasota Bay, Florida, between September 2012 and August 2013. Underwater noise can hinder dolphin communication. The ability of these animals to overcome this obstacle was examined using recorded noise and dolphin whistles. I found that bottlenose dolphins are able to compensate for increased noise in their environment using a wide range of strategies employed in a singular fashion or in various combinations, depending on the frequency content of the noise, noise source, and time of day. These strategies include modifying whistle frequency characteristics, increasing whistle duration, and increasing whistle redundancy. Recordings were also used to evaluate the performance of six recently developed passive acoustic abundance estimation methods, by comparing their results to the true abundance of animals, obtained via a census conducted within the same area and time period. The methods employed were broadly divided into two categories – those involving direct counts of animals, and those involving counts of cues (signature whistles). The animal-based methods were traditional capture-recapture, spatially explicit capture-recapture (SECR), and an approach that blends the “snapshot” method and mark-recapture distance sampling, referred to here as (SMRDS). The cue-based methods were conventional distance sampling (CDS), an acoustic modeling approach involving the use of the passive sonar equation, and SECR. In the latter approach, detection probability was modelled as a function of sound transmission loss, rather than the Euclidean distance typically used. Of these methods, while SMRDS produced the most accurate estimate, SECR demonstrated the greatest potential for broad applicability to other species and locations, with minimal to no auxiliary data, such as distance from sound source to detector(s), which is often difficult to obtain. This was especially true when this method was compared to traditional capture-recapture results, which greatly underestimated abundance, despite attempts to account for major unmodelled heterogeneity. Furthermore, the incorporation of non-Euclidean distance significantly improved model accuracy. The acoustic modelling approach performed similarly to CDS, but both methods also strongly underestimated abundance. In particular, CDS proved to be inefficient. This approach requires at least 3 sensors for localization at a single point. It was also difficult to obtain accurate distances, and the sample size was greatly reduced by the failure to detect some whistles on all three recorders. As a result, this approach is not recommended for marine mammal abundance estimation when few recorders are available, or in high sound attenuation environments with relatively low sample sizes. It is hoped that these results lead to more informed management decisions, and therefore, more effective species conservation.

Development of release methods for critically endangered freshwater pearl mussels (Margaritifera margaritifera)

Biodiversity loss is a global problem with freshwater bivalves considered amongst the most
endangered biota. The freshwater pearl mussel, Margaritifera margaritifera, is declining
throughout its range owing to habitat degradation and overexploitation. In most of its range,
populations are regarded as reproductively non-functional which has led to the development
of captive breeding programmes. A novel method of releasing M. margaritifera was trialled,
with captive-bred juveniles being released into the rivers caged in ‘mussels silos’ (protective
concrete domes with ventilation creating upwelling to ensure water through flow). We
released 240 juvenile mussels and survival and growth rates were monitored for 18 months
post-release for three size classes: A (13.01-20.00mm); B (10.01-13.00mm); and C (4.01-
10.00mm). We explicitly tested two experimental treatments; one where sediment was added
to each silo (allowing mussels to orientate and burrow) and one without sediment. Survival
by the end of the experiment at month 18 was significantly higher for the largest size class at
97% (though growth was lowest in this cohort), and lowest for the smallest size class at 61%
(though growth was highest in this cohort). Survival and growth were unaffected by the
experimental treatment suggesting that adding sediment offered no advantage. Growth was
positively correlated with both water temperature and the particle size of suspended solids
(both of which were collinear, peaking in summer). There are a large number of ex situ
breeding programmes for freshwater pearl mussels throughout Europe and our finding
suggest that the use of ‘mussel silos’ could be a useful tool to protecting juvenile mussels
allowing them to be released at a relatively early stage of development, minimising the risk of
domestication.

Stochastic Modeling of Reversible Biochemical Reaction-Diffusion Systems and High-Resolution Shock-Capturing Methods for Fluid Interfaces

Thesis (Ph.D.)--University of Washington, 2016-08

Creating restoration landscapes: partnerships in large-scale conservation in the UK

It is increasingly recognized that ecological restoration demands conservation action beyond the borders of existing protected areas. This requires the coordination of land uses and management over a larger area, usually with a range of partners, which presents novel institutional challenges for conservation planners. Interviews were undertaken with managers of a purposive sample of large-scale conservation areas in the UK. Interviews were open-ended and analyzed using standard qualitative methods. Results show a wide variety of organizations are involved in large-scale conservation projects, and that partnerships take time to create and demand resilience in the face of different organizational practices, staff turnover, and short-term funding. Successful partnerships with local communities depend on the establishment of trust and the availability of external funds to support conservation land uses. We conclude that there is no single institutional model for large-scale conservation: success depends on finding institutional strategies that secure long-term conservation outcomes, and ensure that conservation gains are not reversed when funding runs out, private owners change priorities, or land changes hands.

A guideline to improve qualitative social science publishing in ecology and conservation journals

A rise in qualitative social science manuscripts published in ecology and conservation journals speaks to the growing awareness of the importance of the human dimension in maintaining and improving Earth’s ecosystems. Given the rise in the quantity of qualitative social science research published in ecology and conservation journals, it is worthwhile quantifying the extent to which this research is meeting established criteria for research design, conduct, and interpretation. Through a comprehensive review of this literature, we aimed to gather and assess data on the nature and extent of information presented on research design published qualitative research articles, which could be used to judge research quality. Our review was based on 146 studies from across nine ecology and conservation journals. We reviewed and summarized elements of quality that could be used by reviewers and readers to evaluate qualitative research (dependability, credibility, confirmability, and transferability); assessed the prevalence of these elements in research published in ecology and conservation journals; and explored the implications of sound qualitative research reporting for applying research findings. We found that dependability and credibility were reasonably well reported, albeit poorly evolved in relation to critical aspects of qualitative social science such as methodology and triangulation, including reflexivity. Confirmability was, on average, inadequately accounted for, particularly with respect to researchers’ ontology, epistemology, or philosophical perspective and their choice of methodology. Transferability was often poorly developed in terms of triangulation methods and the suitability of the sample for answering the research question/s. Based on these findings, we provide a guideline that may be used to evaluate qualitative research presented in ecology and conservation journals to help secure the role of qualitative research and its application to decision making.

Cultural valuation and biodiversity conservation in the Upper Guinea forest, West Africa

The cultural valuation of biodiversity has taken on renewed importance over the last two decades as the ecosystem services framework has become widely adopted. Conservation initiatives increasingly use ecosystem service frameworks to render tropical forest landscapes and their peoples legible to market-oriented initiatives such as REDD+ and biodiversity offsetting schemes. Ecosystem service approaches have been widely criticized by scholars in the social sciences and humanities for their narrow focus on a small number of easily quantifiable and marketable services and a reductionist and sometimes simplistic approach to culture. We address the need to combine methods from each of the “three cultures” of natural science, quantitative social science, and qualitative social science/humanities in conceptualizing the relationship between cultural valuation and biodiversity conservation. We combine qualitative data with forest inventories and a quantitative index of cultural value to evaluate the relationship between cultural valuation and biodiversity conservation in Upper Guinea forest in Liberia, West Africa. Our study focuses on “sacred agroforests,” spaces that are associated with Mande macro-language speaking groups such as the Loma. We demonstrate that sacred agroforests are associated with different cultural values compared with secondary forests. Although biodiversity and biomass are similar, sacred agroforests exhibit a different species composition, especially of culturally salient species, increasing overall landscape agro-biodiversity. Sacred agroforests are also shaped and conserved by local cultural institutions revolving around ancestor worship, ritual, and the metaphysical conceptual category “salɛ.” We conclude that to understand the relationship between cultural valuation and biodiversity conservation, interpretivist approaches such as phenomenology should be employed alongside positivist ecosystem service frameworks.

Seed and vegetative propagation methods for the rare Florida native species Chionanthus pygmaeus (pygmy fringetree)

Chionanthus pygmaeus Small (pygmy fringetree) (Oleaceae) is an endemic and rare Florida species, which has an attractive, small habit giving it great potential for use in managed landscapes. Members of the genus Chionanthus are difficult to propagate via cuttings and possess complex seed dormancies that are not well understood. Conservation of pygmy fringetree and its potential for commercial propagation for use in managed landscapes is contingent on a better understanding of its complex seed dormancy and enhancement of its propagation. I conducted two experiments to assess sexual and asexual propagation methods for pygmy fringetree. The first experiment was conducted to determine what factors are involved in overcoming seed dormancy. Various scarification treatments, which mimicked conditions seeds are exposed to in the wild, were investigated to determine their effects on germination of 20-year-old seeds originally collected from the species’ native range. Treatments included endocarp removal, sulfuric acid, boiling-water, and smoke-water treatments. Prior to treatment initiation, seed viability was estimated to be 12%. Treated seeds went through two cold- and two warm-stratification periods of 4°C and 25°C, respectively, in a dark growth chamber. After 180 days, none of the treatments induced early germination. Seeds were then tested for viability, which was 11%. Seed dormancy of the species is apparently complex, allowing some of the seeds to retain some degree of viability, but without dormancy requirements satisfied. The second experiment was conducted to assess if pygmy fringetree could be successfully propagated via hardwood or root cuttings if the appropriate combination of environmental conditions and hormones were applied. Hardwood and root cuttings were treated with either 1000 ppm IBA talc, 8000 ppm IBA talc, or inert talc. All cuttings were placed on a mist bench in a greenhouse for 9 weeks. Hardwood cuttings were supplemented with bottom heat at 24 °C. No treatments were successful in inducing adventitious root formation. I conclude that pygmy fringetree seeds possess complex dormancy that was not able to be overcome by the treatments utilized. However, this result is confounded by the age of the seeds used in the experiment. I also conclude that vegetative propagation of pygmy fringetree is highly dependent on the time of year cuttings are harvested. Further research of both seed and asexual propagation methods need to be explored before pygmy fringetree can be propagated on a commercial scale.

Sistematic, population genetics, propagation and conservation of Prunus azorica (Rosaceae)

Tese de Doutoramento, Biologia (Ecologia Vegetal), 25 de Junho de 2013, Universidade dos Açores.

Restoration ecology of coastal lagoons: new methods for the prediction of ecological trajectories and economic valuation

Conservation of the seven lagoons of the Palavas complex (southern France) has been severely impaired by nutrient over-enrichment during at least four decades. The effluents of the Montpellier wastewater treatment plant (WWTP) represented the main nutrient input. To improve the water quality of these lagoons, this WWTP was renovated and upgraded and, since the end of 2005, its effluents have been discharged 11 km offshore into the Mediterranean (total investment €150 M). Possibilities of ecosystem restoration as part of a conservation programme were explored by a focus group of experts. Their tasks were: (i) to evaluate the impact of the reduction of the nutrient input; (ii) if necessary, to design additional measures for an active restoration programme; and (iii) to predict ecosystem trajectories for the different cases. Extension of Magnoliophyta meadows can be taken as a proxy for ecosystem restoration as they favour the increase of several fish (seahorse) and bird (ducks, swans, herons) species, albeit they represent a trade-off for greater flamingos. Additional measures for active ecosystem restoration were only recommended for the most impaired lagoon Méjean, while the least impaired lagoon Ingril is already on a trajectory of spontaneous recovery. A multiple contingent valuation considering four different management options for the Méjean lagoon was used in a pilot study based on face-to-face interviews with 159 respondents. Three levels of ecosystem restoration were expressed in terms of recovery of Magnoliophyta meadows, including their impact on emblematic fish and avifauna. These were combined with different options for access (status quo, increasing access, increasing access with measures to reduce disturbance). The results show a willingness of local populations to pay per year about €25 for the highest level of ecological restoration, while they were only willing to allocate about €5 for additional footpaths and hides.

Cryopreservation of somatic embryos for avocado germplasm conservation

Presently avocado germplasm is conserved ex situ in the form of field repositories across the globe including Australia. The maintenance of germplasm in the field is costly, labour and land intensive, exposed to natural disasters and always at the risk of abiotic and biotic stresses. The aim of this study was to overcome these problems using cryopreservation to store avocado (Persea americana Mill.) somatic embryos (SE). Two vitrification-based methods of cryopreservation were optimised (cryovial and droplet-vitrification) using four avocado cultivars (‘A10′, ‘Reed’, ‘Velvick’ and ‘Duke-7′). SE of the four cultivars were stored for short-term (one hour) in liquid nitrogen using the cryovial-vitrification method and showed a viability of 91%, 73%, 86% and 80% respectively. While when using the droplet vitrification method viabilities of 100%, 85% and 93% were recorded for ‘A10′, ‘Reed’ and ‘Velvick’. For long-term storage, SE of cultivars ‘A10′, ‘Reed’ and ‘Velvick’ were successfully recovered with viability of 65–100% after 3 months of LN storage. For cultivar ‘Reed’ and ‘Velvick’ SE were recovered after 12 months of LN storage with viability of 67% and 59%, respectively. The outcome of this work contributes towards the establishment of a cryopreservation protocol that is applicable across multiple avocado cultivars.

Context dependency of trait repeatability and its relevance for management and conservation of fish populations

Repeatability of behavioural and physiological traits is increasingly a focus for animal researchers, for which fish have become important models. Almost all of this work has been done in the context of evolutionary ecology, with few explicit attempts to apply repeatability and context dependency of trait variation toward understanding conservation-related issues. Here, we review work examining the degree to which repeatability of traits (such as boldness, swimming performance, metabolic rate and stress responsiveness) is context dependent. We review methods for quantifying repeatability (distinguishing between within-context and across-context repeatability) and confounding factors that may be especially problematic when attempting to measure repeatability in wild fish. Environmental factors such temperature, food availability, oxygen availability, hypercapnia, flow regime and pollutants all appear to alter trait repeatability in fishes. This suggests that anthropogenic environmental change could alter evolutionary trajectories by changing which individuals achieve the greatest fitness in a given set of conditions. Gaining a greater understanding of these effects will be crucial for our ability to forecast the effects of gradual environmental change, such as climate change and ocean acidification, the study of which is currently limited by our ability to examine trait changes over relatively short time scales. Also discussed are situations in which recent advances in technologies associated with electronic tags (biotelemetry and biologging) and respirometry will help to facilitate increased quantification of repeatability for physiological and integrative traits, which so far lag behind measures of repeatability of behavioural traits.

Chromatographic methods to obtain the biomolecules profile of some aromatic plants irradiated with electron beam

Irradiation is being progressively considered as a versatile and effective conservation technique [1]. Based on this premise, our research group has been investigating the effects of different irradiation conditions in several food matrices. Aromatic plants are among the food products that require suitable conservation technologies to expand their use [2]. The effects of irradiation on the four species (Aloysia citrodora, Melissa officinalis, Melittis melissophyllum and Mentha piperita) studied herein were previously evaluated. In the present study, the same species were treated with different doses of electron-beam irradiation (0, 1 and 10 kGy) and several parameters were evaluated. The individual sugars profile was determined by HPLCRI, fatty acids by GC-FID, organic acids by HPLC-PDA and tocopherols by HPLCfluorescence. In general, the evaluated parameters remained practically unchanged, regardless of plant species or the irradiation dose. Regarding the profile of sugars, the major change was a decrease in the content of disaccharides. The most notable variations in organic acids were observed in plant species with the highest content in these molecules, especially the decrease observed in the samples of M. officinalis and M. melissophyllum. Among the tocopherols, the α and β isoforms were more susceptible to radiation, while the application of 1 kGy tended to increase the levels of tocopherols in Aloysia citrodora, while 10 kGy had the same effect on M. melissophyllum. M. piperita sample showed the highest levels of tocopherols, regardless of the dose applied. Finally, with regard to the fatty acids content, the irradiated samples showed higher percentages of monounsaturated fatty acids than the control samples. In general, analyzing the results taking into account the effects described, it can be concluded that the application of irradiation with electron beam at doses 1 and 10 kGy is an effective way to retain biomolecules profile of the studied species.

Multi-level, Multi-stage and Stochastic Optimization Models for Energy Conservation in Buildings for Federal, State and Local Agencies

Energy Conservation Measure (ECM) project selection is made difficult given real-world constraints, limited resources to implement savings retrofits, various suppliers in the market and project financing alternatives. Many of these energy efficient retrofit projects should be viewed as a series of investments with annual returns for these traditionally risk-averse agencies. Given a list of ECMs available, federal, state and local agencies must determine how to implement projects at lowest costs. The most common methods of implementation planning are suboptimal relative to cost. Federal, state and local agencies can obtain greater returns on their energy conservation investment over traditional methods, regardless of the implementing organization. This dissertation outlines several approaches to improve the traditional energy conservations models. Any public buildings in regions with similar energy conservation goals in the United States or internationally can also benefit greatly from this research. Additionally, many private owners of buildings are under mandates to conserve energy e.g., Local Law 85 of the New York City Energy Conservation Code requires any building, public or private, to meet the most current energy code for any alteration or renovation. Thus, both public and private stakeholders can benefit from this research. The research in this dissertation advances and presents models that decision-makers can use to optimize the selection of ECM projects with respect to the total cost of implementation. A practical application of a two-level mathematical program with equilibrium constraints (MPEC) improves the current best practice for agencies concerned with making the most cost-effective selection leveraging energy services companies or utilities. The two-level model maximizes savings to the agency and profit to the energy services companies (Chapter 2). An additional model presented leverages a single congressional appropriation to implement ECM projects (Chapter 3). Returns from implemented ECM projects are used to fund additional ECM projects. In these cases, fluctuations in energy costs and uncertainty in the estimated savings severely influence ECM project selection and the amount of the appropriation requested. A risk aversion method proposed imposes a minimum on the number of “of projects completed in each stage. A comparative method using Conditional Value at Risk is analyzed. Time consistency was addressed in this chapter. This work demonstrates how a risk-based, stochastic, multi-stage model with binary decision variables at each stage provides a much more accurate estimate for planning than the agency’s traditional approach and deterministic models. Finally, in Chapter 4, a rolling-horizon model allows for subadditivity and superadditivity of the energy savings to simulate interactive effects between ECM projects. The approach makes use of inequalities (McCormick, 1976) to re-express constraints that involve the product of binary variables with an exact linearization (related to the convex hull of those constraints). This model additionally shows the benefits of learning between stages while remaining consistent with the single congressional appropriations framework.

Effects of fishing methods on deep water shark species caught as by-catch off southern Portugal

Deep water sharks are commonly caught as by-catch of longlines targeting bony fishes and trawlers targeting crustaceans in deep water off the southern Portuguese coast. Due to low or no commercial value, these species are most of the times discarded at sea, with only the larger specimens of some species commercialized at very low prices. In this study we present size distributions, maturity distributions, and sex ratios of 2,138 specimens belonging to four different species, namely the lantern sharks Etmopterus pusillus and Etmopterus spinax and the catsharks Galeus melastomus and Galeus atlanticus, caught with these two gears. Trawls generally caught smaller-sized specimens, in a wider length range than longlines. Trawls caught mostly immature specimens of all species, namely 83.7% immature of E. pusillus, 84.3% of E. spinax, 89.5% of G. melastomus, and 95.5% of G. atlanticus, while longlines caught mostly immature E. pusillus (69.2%) and G. melastomus (78.6%) and mostly mature E. spinax (88.2%) and G. atlanticus (87.2%). Trawls tended to catch more males than females of all species except E. spinax, while longlines caught more females than males of E. spinax and G. melastomus and more males than females of the other two species. The main conclusion of this work is that trawls are catching smaller-sized and mostly immature specimens when compared to longlines, meaning that they are probably having a more detrimental effect on these shark populations. The data presented here have significant implications for the conservation of these shark populations since sizes, sexes, and the immature and mature components of the populations are being affected differently by these two fishing gears.

Development of a novel molecular tool for the rapid assessment of the biodiversity changes of benthic nematodes assemblages. Mares Conference Marine Ecosystems Helath and conservation

The molecular profiling system was developed using directed terminal-restriction fragment length polymorphism (dT-RFLP) to characterize soil nematode assemblages by relative abundance of feeding guilds and validation by comparison to traditional morphological method. The good performance of these molecular tools applied to soil nematodes assemblages create an opportunity to develop a novel approach for rapid assessment of the biodiversity changes of benthic nematodes assemblages of marine and estuarine sediments. The main aim of this research is to combine morphological and molecular analysis of estuarine nematodes assemblages, to establish a tool for fast assessment of the biodiversity changes within habitat recovery of Zostera noltii seagrass beds; and validate the dT-RFLP as a high-throughput tool to assess the system recovery. It was also proposed to develop a database of sequences related to individuals identified at species level to develop a new taxonomic reference system. A molecular phylogenetic analysis of the estuarine nematodes has being performed. After morphological identification, barcoding of 18S rDNA are being determined for each nematode species and the results have shown a good degree of concordance between traditional morphology-based identification and DNA sequences. The digest strategy developed for soil nematodes is not suitable for marine nematodes. Then five samples were cloned and sequenced and the sequence data was used to design a new dT-RFLP strategy to adapt this tool to marine assemblages. Several solutions were presented by DRAT and tested empirically to select the solution that cuts most efficiently, separating the different clusters. The results of quantitative PCR showed differences in nematode density between two sampling stations according the abundance of the nematode density obtained by the traditional methods. These results suggest that qPCR could be a robust tool for enumeration of nematode abundance, saving time.