Diversity Patterns of Amphibians in Lowland Amazonian Forests in Southeastern Peru

Biological diversity is threatened worldwide and it is a priority to generate more information that can be used both for understanding ecological processes and determining conservation strategies. For my dissertation, I focused on amphibian diversity patterns in lowland rainforests of southwestern Amazonia to evaluate the importance of habitat heterogeneity in the region. My main purpose was to test the hypothesis that amphibian communities in different forest types differ in species richness, composition, and abundance. I used standardized visual encounter surveys to quantify the species composition and abundance of amphibians at four sites, each containing four forest types (floodplain, terra firme, bamboo, and palm swamp). I used leaf-litter plots to evaluate the effect of soil and leaf-litter characteristics on species richness and abundance of leaf-litter frogs. I intensively sampled at one site and then sampled three other sites (distance among sites varied 3.5-105 km) to evaluate whether the patterns observed at one site were similar elsewhere. I also updated the information on threatened and potentially threatened amphibians in Peru and my study region. I found that no species appears to have experienced population declines in southeastern Peru, suggesting that the region still contains the original species pool. My results support the hypothesis that amphibian communities differ across forest types and that patterns observed at the local scale (one site) are similar at the regional scale (four sites). My data also indicate that there is no correlation between species composition and geographic distance among sites. Instead, an important proportion of the gamma diversity is represented by habitat-related beta diversity. My leaf-litter plot data showed that part of the variation in the leaf-litter community structure is explained by soil and litter characteristics. I found that soil total phosphorus and, to a lesser extent, humidity, leaf-litter mass, and pH is linked to species presence/absence and abundance. My study provides the first standardized, quantitative comparison of amphibian community structure across four major forest types in southwestern Amazonia and highlights the fact that forest types are complementary and necessary for maintaining high species richness in the region.

Massive loggerhead nest predation by ghost crabs in Boavista Island (Cape Verde): implications of the absence of large predators.

[EN] The impact of nest predators on sea turtle hatching success is highly variable depending on predator abundance and also on interactions among different predators. Food web connectivity usually makes it difficult to understand predator-prey interactions and develop efficient conservation strategies. In the Cape Verde archipelago there is an important nesting area for loggerheads where ghost crabs are the only described nest predator. We have studied the impact of ghost crabs on loggerhead nests on this threatened population as well as the efficiency of several management practices to reduce this impact.

Ancient clam gardens, traditional management portfolios, and the resilience of coupled human-ocean systems

Indigenous communities have actively managed their environments for millennia using a diversity of resource use and conservation strategies. Clam gardens, ancient rock-walled intertidal beach terraces, represent one example of an early mariculture technology that may have been used to improve food security and confer resilience to coupled human-ocean systems. We surveyed a coastal landscape for evidence of past resource use and management to gain insight into ancient resource stewardship practices on the central coast of British Columbia, Canada. We found that clam gardens are embedded within a diverse portfolio of resource use and management strategies and were likely one component of a larger, complex resource management system. We compared clam diversity, density, recruitment, and biomass in three clam gardens and three unmodified nonwalled beaches. Evidence suggests that butter clams (Saxidomus gigantea) had 1.96 times the biomass and 2.44 times the density in clam gardens relative to unmodified beaches. This was due to a reduction in beach slope and thus an increase in the optimal tidal range where clams grow and survive best. The most pronounced differences in butter clam density between nonwalled beaches and clam gardens were found at high tidal elevations at the top of the beach. Finally, clam recruits (0.5-2 mm in length) tended to be greater in clam gardens compared to nonwalled beaches and may be attributed to the addition of shell hash by ancient people, which remains on the landscape today. As part of a broader social-ecological system, clam garden sites were among several modifications made by humans that collectively may have conferred resilience to past communities by providing reliable and diverse access to food resources.

The future prospects for the Lake Victoria fishery

The annual fish yields from Lake Victoria have been increasing when the species diversity was dramatically declining. The new fishery is dominated by the introduced predator (Lates niloticus Linne), the exotic herbivore (Oreochromis niloticus Linne) and an indigenous zooplanktivore (Rastrineobola argentea Pellegrin). While the three predominant fish species could sustain the high catch levels, the future viability for the fishery will depend on prudent exploitation regimes and effective management and conservation strategies.

Bananas adrift in time – a case study in the Solomons

Diseases, pests and environmental constraints pose a major threat to the sustainability of banana production globally. To address these challenges, the discovery and study of new sources of genetic resistance and adaptability are required, along with the general conservation of diversity. The Solomon Islands, located in the south-western Pacific region near Papua New Guinea, are a major center of banana diversity. Some collections had been made by nationals of some of the diversity present but little was known internationally of the rich genetic resource present. Two separate visits to the Solomon Islands characterized banana collections, documented and collected germplasm, recommended conservation strategies and provided training in cultivar characterization. A remarkable range of genetic diversity was found, including: many AA and AAA cooking types somewhat like those present in Papua New Guinea; nine Fei cultivars in relatively common usage, and two undescribed wild species as well as five AAB Pacific Plantains and four ABB cooking bananas belonging to the Kalapua subgroup. About six of the unique cultivars were successfully collected and established in the regional in vitro germplasm collection of SPC in Suva, Fiji. Nine Solomon Islanders were trained in the finer points of characterizing banana cultivars. Further collecting and study/evaluation of this rich diversity will promote its appreciation and potential utilization for meeting the challenges and opportunities ahead. Future studies could also determine the spread of the Awawe species and variability of morphological traits in the population. Community-based conservation could promote awareness of dietary diversity for better nutrition, via using the Fei bananas described in this paper. Establishing a virus-free regional field collection could help in comprehensively characterizing and evaluating regional Musa genetic resources. Existing sites could embrace the broader unique diversity of the Solomon Islands, and facilitate sharing this diversity in conjunction with a regional virus-tested in vitro collection.

Evolução da distribuição da lontra (lutra lutra L.) na península ibérica: modelos a diferentes escalas e a sua projeção no espaço e no tempo

A Lontra Euroasiática foi alvo de quatro prospeções na Península Ibérica (1990-2008). Em 2003, foi publicado um modelo de distribuição da lontra, com base nos dados de presença/ausência das prospeções publicadas em 1998. Dadas as suas características, este tipo de modelos pode tornar-se um elemento chave nas estratégias de recuperação da lontra como também, de outras espécies, se comprovada a sua fiabilidade e capacidade de antecipar tendências na distribuição das mesmas. Assim, esta dissertação confrontou as previsões do modelo com os dados de distribuição de 2008, a fim de identificar potências áreas de discordância. Os resultados revelam que, o modelo de distribuição de lontra proposto, apesar de ter por base dados de 1998 e de não considerar explicitamente processos biológicos, conseguiu captar o essencial da relação espécie-ambiente, resultando num bom desempenho preditivo para a distribuição da mesma em Espanha, uma década depois da sua construção; Evolution of otter (Lutra lutra L.) distribution in the Iberian Peninsula: Models at different scales and their projection through space and time Abstract: The Eurasian otter was already surveyed four times in the Iberian Peninsula (1990-2008). In 2003, a distribution model for the otter based on presence/absence data from the survey published in 1998, was published. This type of models has advantages that can make it in a key element for otter conservation strategies and also, for other species, but only, if their reliability and capability to predict species distribution tendencies are validated. The present thesis compares the model predictions with 2008 data, in order to find potential mismatch areas. Results suggest that, although the distribution model for the otter was based on data from 1998 and, doesn’t include explicitly biological mechanisms, it managed to correctly identify the essence of the species-environment relationship, what was translated in a good predictive performance for its actual distribution in Spain, after a decade of its construction.

Highly polymorphic microsatellite markers for the Mediterranean endemic fan mussel Pinna nobilis

Pinna nobilis is an endemic bivalve of the Mediterranean Sea whose populations have decreased in the last decades due to human pressure; as a consequence, it was declared a protected species in 1992. Despite its conservation status, few genetic studies using mitochondrial markers have been published. We report on the isolation and development of 10 microsatellite loci for the fan mussel, Pinna nobilis. All loci (2 di-nucleotide, 5 tri-nucleotide, 2 tetra-nucleotide and 1 penta-nucleotide) are characterized by high levels of polymorphism in 76 individuals tested from two populations in the Balearic Islands (Spain, Western Mediterranean Sea). The number of alleles ranged from 4 to 24 and expected heterozygosity ranged from 0.4269 to 0.9400. These microsatellites could be very useful for the assessment of the genetic diversity and connectivity patterns of P. nobilis and the establishment of new conservation strategies.

Identifying the location of fire refuges in wet forest ecosystems

The increasing frequency of large, high-severity fires threatens the survival of old-growth specialist fauna in fire-prone forests. Within topographically diverse montane forests, areas that experience less severe or fewer fires compared with those prevailing in the landscape may present unique resource opportunities enabling old-growth specialist fauna to survive. Statistical landscape models that identify the extent and distribution of potential fire refuges may assist land managers to incorporate these areas into relevant biodiversity conservation strategies. We used a case study in an Australian wet montane forest to establish how predictive fire simulation models can be interpreted as management tools to identify potential fire refuges. We examined the relationship between the probability of fire refuge occurrence as predicted by an existing fire refuge model and fire severity experienced during a large wildfire. We also examined the extent to which local fire severity was influenced by fire severity in the surrounding landscape. We used a combination of statistical approaches, including generalized linear modeling, variogram analysis, and receiver operating characteristics and area under the curve analysis (ROC AUC). We found that the amount of unburned habitat and the factors influencing the retention and location of fire refuges varied with fire conditions. Under extreme fire conditions, the distribution of fire refuges was limited to only extremely sheltered, fire-resistant regions of the landscape. During extreme fire conditions, fire severity patterns were largely determined by stochastic factors that could not be predicted by the model. When fire conditions were moderate, physical landscape properties appeared to mediate fire severity distribution. Our study demonstrates that land managers can employ predictive landscape fire models to identify the broader climatic and spatial domain within which fire refuges are likely to be present. It is essential that within these envelopes, forest is protected from logging, roads, and other developments so that the ecological processes related to the establishment and subsequent use of fire refuges are maintained.

Urban heritage, development and sustainability: international frameworks, national and local governance

More than half of the world’s population now live in urban areas, and cities provide the setting for contemporary challenges such as population growth, mass tourism and unequal access to socio-economic opportunities. Urban Heritage, Development and Sustainability examines the impact of these issues on urban heritage, considering innovative approaches to managing developmental pressures and focusing on how taking an ethical, inclusive and holistic approach to urban planning and heritage conservation may create a stronger basis for the sustainable growth of cities in the future.This volume is a timely analysis of current theories and practises in urban heritage, with particular reference to the conflict between, and potential reconciliation of, conservation and development goals. A global range of case studies detail a number of distinct practical approaches to heritage on international, national and local scales. Chapters reveal the disjunctions between international frameworks and national implementation and assess how internationally agreed concepts can be misused to justify unsustainable practices or to further economic globalisation and political nationalism. The exclusion of many local communities from development policies, and the subsequent erosion of their cultural heritage, is also discussed, with the collection emphasising the importance of ‘grass roots’ heritage and exploring more inclusive and culturally responsive conservation strategies. Contributions from an international group of authors, including practitioners as well as leading academics, deliver a broad and balanced coverage of this topic. Addressing the interests of both urban planners and heritage specialists, Urban Heritage, Development and Sustainability is an important addition to the field that will encourage further discourse.

The development of 10 novel polymorphic microsatellite markers through next generation sequencing and a preliminary population genetic analysis for the endangered Glenelg spiny crayfish, Euastacus bispinosus

The Glenelg spiny crayfish, Euastacus bispinosus, is an iconic freshwater invertebrate of south eastern Australia and listed as 'endangered' under the Environment Protection and Biodiversity Conservation Act 1999, and 'vulnerable' under the International Union for Conservation of Nature's Red List. The species has suffered major population declines as a result of over-fishing, low environmental flows, the introduction of invasive fish species and habitat degradation. In order to develop an effective conservation strategy, patterns of gene flow, genetic structure and genetic diversity across the species distribution need to be clearly understood. In this study we develop a suite of polymorphic microsatellite markers by next generation sequencing. A total of 15 polymorphic loci were identified and 10 characterized using 22 individuals from the lower Glenelg River. We observed low to moderate genetic variation across most loci (mean number of alleles per locus = 2.80; mean expected heterozygosity = 0.36) with no evidence of individual loci deviating significantly from Hardy-Weinberg equilibrium. Marker independence was confirmed with tests for linkage disequilibrium, and analyses indicated no evidence of null alleles across loci. Individuals from two additional sites (Crawford River, Victoria; Ewens Ponds Conservation Park, South Australia) were genotyped at all 10 loci and a preliminary investigation of genetic diversity and population structure was undertaken. Analyses indicate high levels of genetic differentiation among sample locations (F ST = 0.49), while the Ewens Ponds population is genetically homogeneous, indicating a likely small founder group and ongoing inbreeding. Management actions will be needed to restore genetic diversity in this and possibly other at risk populations. These markers will provide a valuable resource for future population genetic assessments so that an effective framework can be developed for implementing conservation strategies for E. bispinosus.

Genetic analysis along an invasion pathway reveals endemic cryptic taxa, but a single species with little population structure in the introduced range

The invasion pathways of pest arthropods can be traced using genetic tools to develop an understanding of the processes that have shaped successful invasions and to inform both pest management and conservation strategies in their non-native and native ranges, respectively. The redlegged earth mite, Halotydeus destructor, is a major economic pest in Australia, successfully establishing and spreading after arrival from South Africa more than 100 years ago. Halotydeus destructor has recently expanded its range and evolved resistance to numerous pesticides in Australia, raising questions around its origin and spread. Location: South Africa and Australia. Methods: We sampled H. destructor populations in South Africa and Australia and developed a microsatellite marker library. We then examined genetic variation using mtDNA and microsatellite markers across both native and invasive ranges to determine endemic genetic diversity within South Africa, identify the likely origin of invasive populations and test genetic divergence across Australia. Results: The data show that H. destructor comprises a cryptic species complex in South Africa, with putative climatic/host plant associations that may correspond to regional variation. A lineage similar to that found near Cape Town has spread throughout Western and eastern Australia, where populations remain genetically similar. Main conclusions: Tracing the invasion pathway of this economically important pest revealed cryptic lineages in South Africa which points to the need for a taxonomic revision. The absence of significant genetic structure across the wide invasive range of H. destructor within Australia has implications for the development (and spread) of pesticide resistance and also points to recent local adaptation in physiological traits.

Patterns in the space use of the Bearded Reedling, Panurus biarmicus, on the Tay Reedbeds, Scotland

This thesis presents research into the space use of a specialist reedbed Passerine, the Bearded Reedling, or Bearded Tit, Panurus biarmicus, with a view to inform the conservation of this species and reedbeds as a whole. How a species uses space, and how space use changes between individuals or over time, can influence: the ability to forage and hunt effectively, breeding success, susceptibility to predation, genetic health, disease spread, robustness against environmental change and ultimately, colonisation or extinction. Thus, understanding the space use of animals can provide critical insight into ecological systems. Birds offer interesting models when studying animal space use, as, by being intrinsically mobile, many bird species can occupy multiple spatial scales. As a consequence of being completely dependent on patchy and ephemeral reedbed habitats, the Bearded Reedling, has a clustered, inhomogeneous distribution throughout its range. This drives the existence of distinct spatial scales upon which space use studies should be characterised. Distribution and movement within a single reedbed can be considered local-scale, while spatial processes between reedbeds can be considered wide-scale. Temporal processes may act upon both of these scales. For example, changing interactions with predators may influence nest positioning at a local-scale, while seasonal changes in resource requirements might drive processes such as migration at a wide-scale. The Bearded Reedling has a wide temperate breeding range, extending over much of Eurasia. On the IUCN’s red list, it is listed as ‘of least concern’, with an estimated European population between 240,000-480,000 breeding pairs. Despite its relatively favourable conservation status, its dependence on reedbed habitats drives a fragmented distribution, with populations being concentrated in small, isolated, stands. Over the last century reedbed wetlands have suffered rapid declines caused by drainage schemes undertaken to improve land for development or agriculture. Additionally, many remaining reed stands are subject to extensive commercial management to produce thatch or biofuel. Conversely, in other areas, management is driven by conservation motives which recognise the present threats to reedbeds, and aim to encourage the diversity of species associated with these habitats. As the Bearded Reedling is fundamentally linked to the quality and structure of a reed stand, understanding the space use of this species will offer information for the direct conservation of this specialist species, and for the effects of reedbed management as a whole. This thesis first presents studies of space use at a local-scale. All local-scale research is conducted at the Tay Reedbeds in eastern Scotland. Mist netting and bird ringing data are used within capture recapture models, which include an explicit spatial component, to gain insight into the abundance of the Bearded Reedling on the Tay. This abundance estimation approach suggests the Tay reedbeds are a stronghold for this species on the British Isles, and that, as a high latitude site, the Tay may have importance for range expansion. A combination of transect surveys and radio-tracking data are then used to establish the local-scale space use of this species during the breeding and autumnal seasons. These data are related to changes in the structure of reed caused by local management in the form of mosaic winter reed cutting. Results suggest that birds exploit young and cut patches of reed as foraging resources when they are available, and that old, unmanaged reed is critical for nesting and winter foraging. Further local-scale studies concern the spatial patterns in the nesting habits of this species. Mosaic reed cutting creates clear edges in a reedbed. Artificial nests placed in the Tay Reedbeds demonstrate increased nest predation rates closer to the edges of cut patches. Additionally, high predation rates become reduced as the cut reed re-grows, suggesting that reed cutting may increase accessibility of the stand to predators. As Bearded Reedling nests are uncommon and difficult to locate, the timing, site selection and structure of a sample of real nests from the Tay is then detailed. These demonstrate an early, and relatively rigid breeding onset in this species, the importance of dense, compacted reeds as nesting sites and a degree of flexibility in nest structure. Conservation efforts will also benefit from studies into wide-scale spatial processes. These may be important when establishing how colonisation events occur and when predicting the effects of climatic change. The Bearded Reedling has been traditionally considered a resident species which only occasionally undertakes wide-scale, between-reedbed, movements. Indeed, the ecology of this species suggests strict year round local residency to reedbeds, with distinct seasonal changes in diet allowing occupation of these habitats year round. The European ringing recoveries of this species, since the 1970s are investigated to better characterise the wider movements of specialist resident. These suggest residency in southern populations, but higher instances of movement than expected in more northerly regions. In these regions wide-scale movement patterns resemble those of partial regular migratory species. An understanding of local and wide-scale spatial processes can offer a strong foundation on which to build conservation strategies. This thesis aims to use studies of space use to provide this foundation for the Bearded Reedling and offer further insight into the ecology of reedbed habitats as a whole. The thesis concludes by proposing an effective strategy for the conservation management of reedbeds that will especially benefit the Bearded Reedling.