The selection of biodiversity indicators for business landholdings

Businesses are seen as the next stage in delivering biodiversity improvements linked to local and UK Biodiversity Action Plans. Global discussion of biodiversity continues to grow, with the Millennium Ecosystem Assessment, updates to the Convention on Biological Diversity and The Economics of Ecosystems and Biodiversity being published during the time of this project. These publications and others detail the importance of biodiversity protection and also the lack of strategies to deliver this at an operational level. Pressure on UK landholding businesses is combined with significant business opportunities associated with biodiversity engagement. However, the measurement and reporting of biodiversity by business is currently limited by the complexity of the term and the lack of suitable procedures for the selection of metrics. Literature reviews identified confusion surrounding biodiversity as a term, limited academic literature regarding business and choice of biodiversity indicators. The aim of the project was to develop a methodology to enable companies to identify, quantify and monitor biodiversity. Research case studies interviews were undertaken with 10 collaborating organisations, selected to represent =best practice‘ examples and various situations. Information gained through case studies was combined with that from existing literature. This was used to develop a methodology for the selection of biodiversity indicators for company landholdings. The indicator selection methodology was discussed during a second stage of case study interviews with 4 collaborating companies. The information and opinions gained during this research was used to modify the methodology and provide the final biodiversity indicator selection methodology. The methodology was then tested through implementation at a mineral extraction site operated by a multi-national aggregates company. It was found that the methodology was a suitable process for implementation of global and national systems and conceptual frameworks at the practitioner scale. Further testing of robustness by independent parties is recommended to improve the system.

Linking herbivory and pollination: Costs and selection implications in Centrosema virginianum Bentham (Fabaceae: Papilionoideae)

This research first evaluated levels and type of herbivory experienced by Centrosema virginianum plants in their native habitat and how florivory affected the pollinator activity. I found that populations of C. virginianum in two pine rockland habitat fragments experienced higher herbivory levels (15% and 22%) compared with plants in the protected study site (8.6%). I found that bees (Hymenoptera) pollinated butterfly pea. Furthermore, I found that florivores had a negative effect in the pollinators visitation rates and therefore in the seed set of the population. ^ I then conducted a study using a greenhouse population of C. virginianum. I applied artificial herbivory treatments: control, mild herbivory and severe herbivory. Flower size, pollen produced, ovules produced and seeds produced were negatively affected by herbivory. I did not find difference in nectar volume and quality by flowers among treatments. Surprisingly, severely damaged plants produced flowers with larger pollen than those from mildly damaged and undamaged plants. Results showed that plants tolerated mild and severe herbivory with 6% and 17% reduction of total fitness components, respectively. However, the investment of resources was not equisexual. ^ A comparison in the ability of siring seeds between large and small pollen was necessary to establish the biological consequence of size in pollen performance. I found that fruits produced an average of 18.7 ± 1.52 and 17.7 ± 1.50 from large and small pollen fertilization respectively. These findings supported a pollen number-size trade-off in plants under severe herbivory treatments. As far as I know, this result has not previously been reported. ^ Lastly, I tested how herbivory influenced seed abortion patterns in plants, examining how resources are allocated on different regions within fruits under artificial herbivory treatments. I found that self-fertilized fruits had greater seed abortion rates than cross-fertilized fruits. The proportion of seeds aborted was lower in the middle regions of the fruits in cross-fertilized fruits, producing more vigorous progeny. Self-fertilized fruits did not show patterns of seedling vigor. I also found that early abortion was higher closer to the peduncular end of the fruits. Position of seeds within fruits could be important in the seed dispersion mechanism characteristic of this species. ^

Prioritizing tropical habitats for long-distance migratory songbirds: an assessment of habitat quality at a stopover site in Colombia

Long-distance migratory birds are declining globally and migration has been identified as the primary source of mortality in this group. Despite this, our lack of knowledge of habitat use and quality at stopovers, i.e., sites where the energy for migration is accumulated, remains a barrier to designing appropriate conservation measures, especially in tropical regions. There is therefore an urgent need to assess stopover habitat quality and concurrently identify efficient and cost-effective methods for doing so. Given that fuel deposition rates directly influence stopover duration, departure fuel load, and subsequent speed of migration, they are expected to provide a direct measure of habitat quality and have the advantage of being measurable through body-mass changes. Here, we examined seven potential indicators of quality, including body-mass change, for two ecologically distinct Neotropical migratory landbirds on stopover in shade-coffee plantations and tropical humid premontane forest during spring migration in Colombia: (1) rate of body-mass change; (2) foraging rate; (3) recapture rate; (4) density; (5) flock size; (6) age and sex ratios; and (7) body-mass distribution. We found higher rates of mass change in premontane forest than in shade-coffee in Tennessee Warbler Oreothlypis peregrina, a difference that was mirrored in higher densities and body masses in forest. In Gray-cheeked Thrush Catharus minimus, a lack of recaptures in shade-coffee and higher densities in forest, also suggested that forest provided superior fueling conditions. For a reliable assessment of habitat quality, we therefore recommend using a suite of indicators, taking into account each species’ ecology and methodological considerations. Our results also imply that birds stopping over in lower quality habitats may spend a longer time migrating and require more stopovers, potentially leading to important carryover effects on reproductive fitness. Evaluating habitat quality is therefore imperative prior to defining the conservation value of newly identified stopover regions.

Water chemistry, carbonate system parameters, and macro-organism biomass of vent and off-vent sites in the Columbretes Islands Marine Reserve

Ocean acidification is receiving increasing attention because of its potential to affect marine ecosystems. Rare CO2 vents offer a unique opportunity to investigate the response of benthic ecosystems to acidification. However, the benthic habitats investigated so far are mainly found at very shallow water (less than or equal to 5 m depth) and therefore are not representative of the broad range of continental shelf habitats. Here, we show that a decrease from pH 8.1 to 7.9 observed in a CO2 vent system at 40 m depth leads to a dramatic shift in highly diverse and structurally complex habitats. Forests of the kelp Laminaria rodriguezii usually found at larger depths (greater than 65 m) replace the otherwise dominant habitats (i.e. coralligenous outcrops and rhodolith beds), which are mainly characterized by calcifying organisms. Only the aragonite-calcifying algae are able to survive in acidified waters, while high-magnesium-calcite organisms are almost completely absent. Although a long-term survey of the venting area would be necessary to fully understand the effects of the variability of pH and other carbonate parameters over the structure and functioning of the investigated mesophotic habitats, our results suggest that in addition of significant changes at species level, moderate ocean acidification may entail major shifts in the distribution and dominance of key benthic ecosystems at regional scale, which could have broad ecological and socio-economic implications.

Phocid seal leptin: tertiary structure and hydrophobic receptor binding site preservation during distinct leptin gene evolution

The cytokine hormone leptin is a key signalling molecule in many pathways that control physiological functions. Although leptin demonstrates structural conservation in mammals, there is evidence of positive selection in primates, lagomorphs and chiropterans. We previously reported that the leptin genes of the grey and harbour seals (phocids) have significantly diverged from other mammals. Therefore we further investigated the diversification of leptin in phocids, other marine mammals and terrestrial taxa by sequencing the leptin genes of representative species. Phylogenetic reconstruction revealed that leptin diversification was pronounced within the phocid seals with a high dN/dS ratio of 2.8, indicating positive selection. We found significant evidence of positive selection along the branch leading to the phocids, within the phocid clade, but not over the dataset as a whole. Structural predictions indicate that the individual residues under selection are away from the leptin receptor (LEPR) binding site. Predictions of the surface electrostatic potential indicate that phocid seal leptin is notably different to other mammalian leptins, including the otariids. Cloning the grey seal leptin binding domain of LEPR confirmed that this was structurally conserved. These data, viewed in toto, support a hypothesis that phocid leptin divergence is unlikely to have arisen by random mutation. Based upon these phylogenetic and structural assessments, and considering the comparative physiology and varying life histories among species, we postulate that the unique phocid diving behaviour has produced this selection pressure. The Phocidae includes some of the deepest diving species, yet have the least modified lung structure to cope with pressure and volume changes experienced at depth. Therefore, greater surfactant production is required to facilitate rapid lung re-inflation upon surfacing, while maintaining patent airways. We suggest that this additional surfactant requirement is met by the leptin pulmonary surfactant production pathway which normally appears only to function in the mammalian foetus.

Conservation value, biodiversity value and methods of assessment in regenerating and human disturbed tropical forest

Although the value of primary forests for biodiversity conservation is well known, the potential biodiversity and conservation value of regenerating forests remains controversial. Many factors likely contribute to this, including: 1. the variable ages of regenerating forests being studied (often dominated by relatively young regenerating forests); 2. the potential for confounding on-going human disturbance (such as logging and hunting); 3. the relatively low number of multi-taxa studies; 4. the lack of studies that directly compare different historic disturbances within the same location; 5. contrasting patterns from different survey methodologies and the paucity of knowledge on the impacts across different vertical levels of rainforest biodiversity (often due to a lack of suitable methodologies available to assess them). We also know relatively little as to how biodiversity is affected by major current impacts, such as unmarked rainforest roads, which contribute to this degradation of habitat and fragmentation. This thesis explores the potential biodiversity value of regenerating rainforests under the best of scenarios and seeks to understand more about the impact of current human disturbance to biodiversity; data comes from case studies from the Manu and Sumaco Biosphere Reserves in the Western Amazon. Specifically, I compare overall biodiversity and conservation value of a best case regenerating rainforest site with a selection of well-studied primary forest sites and with predicted species lists for the region; including a focus on species of key conservation concern. I then investigate the biodiversity of the same study site in reference to different types of historic anthropogenic disturbance. Following this I investigate the impacts to biodiversity from an unmarked rainforest road. In order to understand more about the differential effects of habitat disturbance on arboreal diversity I directly assess how patterns of butterfly biodiversity vary between three vertical strata. Although assessments within the canopy have been made for birds, invertebrates and bats, very few studies have successfully targeted arboreal mammals. I therefore investigate the potential of camera traps for inventorying arboreal mammal species in comparison with traditional methodologies. Finally, in order to investigate the possibility that different survey methodologies might identify different biodiversity patterns in habitat disturbance assessments, I investigate whether two different but commonly used survey methodologies used to assess amphibians, indicate the same or different responses of amphibian biodiversity to historic habitat change by people. The regenerating rainforest study site contained high levels of species richness; both in terms of alpha diversity found in nearby primary forest areas (87% ±3.5) and in terms of predicted primary forest diversity from the region (83% ±6.7). This included 89% (39 out of 44) of the species of high conservation concern predicted for the Manu region. Faunal species richness in once completely cleared regenerating forest was on average 13% (±9.8) lower than historically selectively logged forest. The presence of the small unmarked road significantly altered levels of faunal biodiversity for three taxa, up to and potentially beyond 350m into the forest interior. Most notably, the impact on biodiversity extended to at least 32% of the whole reserve area. The assessment of butterflies across strata showed that different vertical zones within the same rainforest responded differently in areas with different historic human disturbance. A comparison between forest regenerating after selective logging and forest regenerating after complete clearance, showed that there was a 17% greater reduction in canopy species richness in the historically cleared forest compared with the terrestrial community. Comparing arboreal camera traps with traditional ground-based techniques suggests that camera traps are an effective tool for inventorying secretive arboreal rainforest mammal communities and detect a higher number of cryptic species. Finally, the two survey methodologies used to assess amphibian communities identified contrasting biodiversity patterns in a human modified rainforest; one indicated biodiversity differences between forests with different human disturbance histories, whereas the other suggested no differences between forest disturbance types. Overall, in this thesis I find that the conservation and biodiversity value of regenerating and human disturbed tropical forest can potentially contribute to rainforest biodiversity conservation, particularly in the best of circumstances. I also highlight the importance of utilising appropriate study methodologies that to investigate these three-dimensional habitats, and contribute to the development of methodologies to do so. However, care should be taken when using different survey methodologies, which can provide contrasting biodiversity patterns in response to human disturbance.

Influence of phosphine resistance genes on flight propensity and resource location in Tribolium castaneum (Herbst) (Coleoptera: Tenebrionidae): the landscape for selection

Phosphine resistance in Tribolium castaneum Herbst (Coleoptera: Tenebrionidae) has evolved through changes to enzymes involved in basic metabolic pathways. These changes impose metabolic stress and could affect energy-demanding behaviours. We therefore tested whether phosphine resistance alleles impact the movement of these insects in their quest for new resources. We measured walking and flight parameters of four T. castaneum genotypes: (1) a field-derived population, (2) a laboratory cultured, phosphine-susceptible reference strain, (3) a laboratory cultured, phosphine-resistant reference strain, and (4) a resistant introgressed strain that is almost identical genetically to the susceptible population. The temporal pattern of flight was identical across all populations, but resistant beetles took flight significantly less, walked more slowly, and located resources less successfully than did susceptible beetles. Also, the field-derived beetles (proved not to be carrying resistance genes) walked significantly faster and more directly towards food resources, and had a higher propensity for flight when compared to the susceptible laboratory beetles. These negative effects suggest survival of beetles with the resistance alleles will be compromised should they leave phosphine application sites. The field for selection therefore extends beyond the site at which phosphine fumigant imposed its effect, and other mutations are also likely to be affected in this way.

Sea otter predation and the distribution of bivalve prey in the Elkhorn Slough National Estuarine Research Reserve

The California sea otter population is gradually expanding in size and geographic range and is consequently invading new feeding grounds, including bays and estuaries that are home to extensive populations of bivalve prey. One such area is the Elkhorn Slough, where otters have apparently established a spring and summer communal feeding and resting area. In anticipation of future otter foraging in the slough, an extensive baseline database on bivalve densities, size distributions, biomasses, and burrow depths has been established for three potential bivalve prey species, Saxidomus nuttalli, Tresus nutallii, and Zirphaea pilsbryi. In 1986, the Elkhorn Slough otters were foraging predominately at two areas immediately east and west of the Highway 1 bridge (Skipper's and the PG&E Outfall). Extensive subtidal populations of Saxidomus nuttalli and Tresus nuttallii occur in these areas. Shell records collected at these study areas indicated that sea otters were foraging selectively on Saxidomus over Tresus. The reason for this apparent preference was not clear. At the Skipper's study site, 51% of the shell record was composed of Saxidomus, yet this species accounted for only 16% of the in situ biomass, and only 39% of the available clams. Tresus represented 49% of the shell record at Skipper's, yet this species accounted for 84% of the in situ biomass and 61% of the available clams. There was no difference in mean burrow depth between the two species at this site so availability does not explain the disparity in consumption. At the PG&E Outfall, Saxidomus represents 66% of the in situ biomass and 81% of the available clams, while Tresus accounts for 34% of the in situ biomass and 19% of the available clams. Saxidomus accounts for 96% of the shell record at this site vs. 4% for Tresus, again indicating that the otters were preying on Saxidomus out of proportion to their density or biomass. High densities and biomasses of a third species, Zirphaea pilsbryi, occur in areas where sea otters were observed to be foraging, yet no cast-off Zirphaea shells were found. Although it is possible this species was not represented in the shell record because the otters were simply chewing up the shells, it is more likely this species is avoided by sea otters. There were relatively few sea otters in the Elkhorn Slough in 1986 compared to the previous two years. This, coupled with high bivalve densities, precluded any quantitative comparison of bivalve densities before and after the 1986 sea otter occupation. Qualitative observations made during the course of this study, and quantitative observations from previous studies indicate that, after 3 years, sea otters are not yet significantly affecting bivalve densities in the Elkhorn Slough.

L’industrie osseuse des Iroquoiens du site Mailhot-Curran (BgFn-2) : une étude des déchets de fabrication

Bien que l’os soit une matière première ayant joué un rôle essentiel au sein des activités quotidiennes des Iroquoiens du Saint-Laurent, il existe à ce jour très peu d’analyses systématiques de l’outillage en os et des débris de fabrication retrouvés en Iroquoianie. Afin de pallier ces lacunes, ce mémoire de maitrise porte sur l’analyse des vestiges en os ouvragés récupérés sur le site villageois Mailhot-Curran (BgFn-2), occupé durant le Sylvicole supérieur tardif par une communauté iroquoienne du Saint-Laurent. Plus précisément, l’étude consiste à analyser l’industrie osseuse en portant une attention particulière aux déchets de fabrication. Cet examen attentif a pour principal objectif de documenter les modes de gestion et de sélection de la matière première ainsi que d’améliorer la compréhension des techniques préhistoriques employées pour la fabrication des objets en os. Au moyen d’analyses technologiques, zooarchéologiques et tracéologiques, il sera possible de classifier les déchets de fabrication, de documenter leur origine technologique et, ultimement, de reconstituer un certain nombre de chaines opératoires. Une étude détaillée de la distribution spatiale des artéfacts permettra également de mieux comprendre l’organisation des activités dans l’espace villageois. Ce mémoire a aussi pour objectif de fournir des balises méthodologiques et empiriques relatives à l’étude des déchets de fabrications en os, afin de démontrer la pertinence de considérer ces derniers dans la compréhension des systèmes socioéconomiques et culturels.

L’industrie osseuse des Iroquoiens du site Mailhot-Curran (BgFn-2) : une étude des déchets de fabrication

Bien que l’os soit une matière première ayant joué un rôle essentiel au sein des activités quotidiennes des Iroquoiens du Saint-Laurent, il existe à ce jour très peu d’analyses systématiques de l’outillage en os et des débris de fabrication retrouvés en Iroquoianie. Afin de pallier ces lacunes, ce mémoire de maitrise porte sur l’analyse des vestiges en os ouvragés récupérés sur le site villageois Mailhot-Curran (BgFn-2), occupé durant le Sylvicole supérieur tardif par une communauté iroquoienne du Saint-Laurent. Plus précisément, l’étude consiste à analyser l’industrie osseuse en portant une attention particulière aux déchets de fabrication. Cet examen attentif a pour principal objectif de documenter les modes de gestion et de sélection de la matière première ainsi que d’améliorer la compréhension des techniques préhistoriques employées pour la fabrication des objets en os. Au moyen d’analyses technologiques, zooarchéologiques et tracéologiques, il sera possible de classifier les déchets de fabrication, de documenter leur origine technologique et, ultimement, de reconstituer un certain nombre de chaines opératoires. Une étude détaillée de la distribution spatiale des artéfacts permettra également de mieux comprendre l’organisation des activités dans l’espace villageois. Ce mémoire a aussi pour objectif de fournir des balises méthodologiques et empiriques relatives à l’étude des déchets de fabrications en os, afin de démontrer la pertinence de considérer ces derniers dans la compréhension des systèmes socioéconomiques et culturels.

Occurrence of OsHV-1 in Crassostrea gigas cultured in Ireland during an exceptionally warm summer. Selection of less susceptible oysters

The occurrence of OsHV-1, a herpes virus causing mass mortality in the Pacific oyster Crassostrea gigas was investigated with the aim to select individuals with different susceptibility to the infection. Naïve spat transferred to infected areas and juveniles currently being grown at those sites were analyzed using molecular and histology approaches. The survey period distinguishes itself by very warm temperatures reaching up to 3.5°C above the average. The virus was not detected in the virus free area although a spread of the disease could be expected due to high temperatures. Overall mortality, prevalence of infection and viral load was higher in spat confirming the higher susceptibility in early life stages. OsHV-1 and oyster mortality were detected in naïve spat after 15 days of cohabitation with infected animals. Although, infection was associated with mortality in spat, the high seawater temperatures could also be the direct cause of mortality at the warmest site. One stock of juveniles suffered an event of abnormal mortality that was significantly associated with OsHV-1 infection. Those animals were infected with a previously undescribed microvariant whereas the other stocks were infected with OsHV-1 μVar. Cell lesions due to the infection were observed by histology and true infections were corroborated by in situ hybridization. Survivors from the natural outbreak were exposed to OsHV-1 μVar by intramuscular injection and were compared to naïve animals. The survival rate in previously exposed animals was significantly higher than in naïve oysters. Results derived from this study allowed the selection of animals that might possess interesting characteristics for future analysis on OsHV-1 resistance.

Early reserve effects linked to small home ranges of a commercial fish, Diplodus sargus, Sparidae

Studies that combine both the ecological responses of marine species and protection measures with movement patterns and habitat use are of major importance in order to better understand the performance of marine protected areas (MPA) and how species respond to their implementation. However, few studies have assessed MPA performance by relating local individual movement patterns and the observed reserve effects. In this study, we combined acoustic telemetry with abundance estimates to study the early effects of a recently established small coastal MPA on the local populations of white seabream. The results show that even small, recently established coastal MPAs can increase the abundance and biomass of commercial fish species, provided that target species have small home ranges and exhibit high site fidelity.

Sexual selection in a tropical fruit fly : role of a plant derived chemical in mate choice

The specific mechanisms by which selective pressures affect individuals are often difficult to resolve. In tephritid fruit flies, males respond strongly and positively to certain plant derived chemicals. Sexual selection by female choice has been hypothesized as the mechanism driving this behaviour in certain species, as females preferentially mate with males that have fed on these chemicals. This hypothesis is, to date, based on studies of only very few species and its generality is largely untested. We tested the hypothesis on different spatial scales (small cage and seminatural field-cage) using the monophagous fruit fly, Bactrocera cacuminata. This species is known to respond to methyl eugenol (ME), a chemical found in many plant species and one upon which previous studies have focused. Contrary to expectation, no obvious female choice was apparent in selecting ME-fed males over unfed males as measured by the number of matings achieved over time, copulation duration, or time of copulation initiation. However, the number of matings achieved by ME-fed males was significantly greater than unfed males 16 and 32 days after exposure to ME in small cages (but not in a field-cage). This delayed advantage suggests that ME may not influence the pheromone system of B. cacuminata but may have other consequences, acting on some other fitness consequence (e.g., enhancement of physiology or survival) of male exposure to these chemicals. We discuss the ecological and evolutionary implications of our findings to explore alternate hypotheses to explain the patterns of response of dacine fruit flies to specific plant-derived chemicals.