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A key challenge in biodiversity is: How many species are there on earth? This issue is especially acute in poorly surveyed regions with high diversity, particularly Southeast Asia that also experiences many limitations such as lack of funds, documents and experts. To help meet this challenge, I have developed a five-tiered approach for diversity measurement of freshwater fish for use in Thailand. This is: (1) the creation of a newly updated species inventory that uses existing data; (2) exploration of the patterns of species richness, endemism, and uniqueness; (3) estimation of the total species richness; (4) investigation of patterns of rarity; and (5) integration of this knowledge into conservation practice. The system should be applicable to other regions and other taxa where a similar challenge exists. My work shows that eight hundred and seventy-two species in 17 orders, 55 families and 255 genera of freshwater fishes, accounting for roughly 10% of the world's freshwater fish diversity, have been reported for Thailand to date. This number was derived from information in the museum collections, literature and all other available sources, including reports written in Thai as well as in English. During this work I uncovered many gaps in biodiversity information, in terms of taxonomic and spatial records, though some families and basins are better represented than others. Taxonomic uncertainty also continues to be a challenge for taxonomists and users. The high diversity of freshwater fishes in Thailand is the result of both high alpha (α) diversity (diversity within a particular locality) and beta (β) diversity (diversity differences between localities). I concluded that the substantial beta diversity I detected is associated with the geographical separation of the six river basins in Thailand. For example, the species composition of freshwater fishes in the Salween Basin dramatically differs from all other basins of Thailand. In contrast, the Chao Phraya Basin and the Mekong Basin contain the greatest number of shared species. Approximately 55% of species have a wide distribution range (being reported from more than two basins), whereas 45% are highly restricted within a single basin. Analyses using species richness estimators suggest that the figure of 872 species is an underestimate and that there may be between 1000 and 1300 fish species in Thailand, in other words an increase of between 14.7% and 49.1% over the list I compiled (which is itself an increase of 52.2% over the last report in 1997). Freshwater fish have become increasingly vulnerable to anthropogenic activities. Of the 872 Thai fish species, 6.8% and 15.1% are globally and nationally threatened, respectively. Nonetheless, a striking feature of the database is that the conservation status of the vast majority of species has not so far been assessed, either globally or nationally. Scientists and policy makers will find these results useful in appreciating the magnitude of the tasks involved in surveying, describing and conserving the country's freshwater fish biota. My work highlights localities and taxa where conservation is a priority and is thus an important resource for policy makers and conservation planners concerned with the management of freshwater fish in Thailand.

Magister Scientiae (Biodiversity and Conservation Biology) - MSc (Biodiv and Cons Biol) / Knowledge of global reptile ecology is limited and there remains much to understand in terms of detailed reptile species information, including that of their distributions. In South Africa, despite being one of SANParks best-studied reserves, surprisingly little is known about the distributions and spatial ecology of reptiles within Kruger National Park (KNP). Management within KNP follows a strategic adaptive management strategy which monitors the statuses of animals using species or group specific indicators. Indicators are given predetermined upper and lower ranges of acceptable fluctuation before actions are taken. These ranges are referred to as thresholds of potential concern (TPCs), and for reptiles these are based on changes to their distributions across the landscape of KNP. An apparent lack of high-quality reptile distribution data inhibits the effective monitoring of the statuses of these animals within KNP, which in turn limits management and conservation options. In this study, I use several methods to quantify available reptile occurrence data which formed the foundations for predicting the distributions of these species across KNP by means of species distribution modelling, with a view to gaining novel insight into reptile assemblage structure across the landscape of KNP.

A dissertation submitted to the Faculty of Science, University of the Witwatersrand, Johannesburg, in fulfilment of requirements for the degree of Master of Science. Johannesburg, 14 December 2016. / The interaction between business and biodiversity has seen growing importance in corporate management; impacting policy, practices and strategy. This study examines South African companies’ assimilation of recommended biodiversity management practices, as communicated through their annual reporting and official websites. A selection of nine South African companies in the forestry, sugar and mining sectors were studied with regards to their reporting on biodiversity management practices. The research aimed to understand the extent of structured approach to biodiversity management, and explore potential sectorial differences. The study found a wide acceptance of the UN Global Compact Principles, the GRI reporting guidelines and the King Code of good governance principles. However, the companies did not demonstrate a consistent governance structure for biodiversity management. The study revealed one mining company with a stronger biodiversity governance structure making the use of various dedicated policies and standards. Furthermore, the study identified few sector specific differences. Though the forestry sector demonstrated good practice with its emphasis on biodiversity in its supply chain management. The study did not reveal a particular uptake of emerging biodiversity concepts such as No Net Loss, payment for ecosystem services or agroforestry, however the companies had adopted several sustainability and governance recommendations and standards. The study did not identify the existence, nor the use, of dedicated biodiversity certification programmes or South African developed cross-sector biodiversity certification programmes. The finance sector is in a good position to positively influence corporate biodiversity management practices. However, the study results give an impression that there is untapped potential in the finance sector to further drive the biodiversity management agenda in South Africa. Keywords: Corporate Biodiversity Management, Biodiversity Management Framework, Biodiversity Best Practices, / LG2017

Studies in agricultural landscapes have shown that anthropogenic environments may be relevant to wildlife species. Given the extent of these areas efficient research methods are needed to assess its ecological value in terms of local diversity, such as the use of biological indicators. The main goal here was to evaluate the possible relationship between the native vegetation biomass and diversity of small mammals in a silvicultural landscape of São Paulo. The study was developed at Fazenda Três Lagoas, which is part of the \"Programa de Pesquisa em Biodiversidade\" (PPBio), at Angatuba municipality, State of São Paulo, and lasted nine months. From May 2015 to March 2016 nine sampling campaigns were carried over a grid of 15 pitfall traps, five in Eucalyptus plantations, five in native vegetation and five in abandoned pastures. In the Chapter 1 the distribution and abundance patterns of small mammals on a silvicultural landcape during the early second cycle of Eucalyptus plantation in Southeastern Brazil was evaluated. A total of 672 individuals from 15 species of the orders Rodentia (9 spp.) and Didelphimorphia (6 spp.) were captured and five new species were detected in the study area in comparison to the first cycle. Although these species are predominantly generalists, there were differences in the abundance of small mammals in the three environments. The presence of native vegetation patches associated with riparian areas and abandoned pastures and the role of small mammals as a food resource for predators on a trophic structure, gives a certain conservation value to silvicultural landscapes in southeastern Brazil. In the Chapter 2 the relationship between landscape metrics and patterns of diversity, distribution and abundance of small mammals in a silvicultural landscape were evaluated. The species richness and family diversity of small mammals have been predominantly determined by the percentage of native vegetation. However, the abundance of small mammals can be determined by an indirect estimate of the native vegetation biomass (i.e., NDVI), which can be considered a 3D landscape metric as it is related to volume. Therefore, to succeed in assessing the value of agricultural landscape, future studies should consider landscape context, as well as the landscape metrics associated with geospatial data analysis and the distinct responses of species. / Estudos em paisagens agrícolas têm mostrado que ambientes antrópicos podem ser relevantes para muitas espécies selvagens. Dada a extensão destas áreas, são necessários métodos eficientes de pesquisa para avaliar seu valor ecológico em termos de diversidade local, tais como o uso de indicadores biológicos. O presente estudo teve como objetivo geral avaliar a possível relação entre a biomassa de vegetação nativa e a diversidade de mamíferos de pequeno porte em uma paisagem silvicultural do estado de São Paulo. O estudo foi desenvolvido na Fazenda Três Lagoas, que é parte do Núcleo Angatuba do Programa de Pesquisa em Biodiversidade (PPBio), no município de Angatuba, Estado de São Paulo e teve a duração de nove meses. De maio de 2015 a março de 2016, foram realizadas campanhas mensais de amostragem em uma grade amostral com 15 conjuntos de armadilhas de interceptação e queda (pitfall), sendo cinco nas plantações de Eucalyptus spp., cinco em vegetação nativa e cinco em pasto abandonado. No Capítulo 1 foram avaliados os padrões de distribuição e abundância de pequenos mamíferos em uma paisagem silvicultural ao início do segundo ciclo de plantações de Eucalyptus no Sudeste do Brasil. Um total de 672 indivíduos de 15 espécies das ordens Rodentia (9 spp.) e Didelphimorphia (6 spp.) foram capturados e cinco novas espécies foram detectadas na área de estudo em relação ao primeiro ciclo. Embora as espécies presentes sejam predominantemente generalistas, houve diferença na abundância de pequenos mamíferos nos três ambientes. A presença de fragmentos de vegetação nativa associados a áreas ripícolas e pasto abandonado e o papel dos pequenos mamíferos como recurso alimentar para predadores em uma estrutura trófica, atribui um valor de conservação às paisagens silviculturais no sudeste do Brasil. No Capítulo 2, o objetivo foi avaliar a relação entre métricas da paisagem e padrões de diversidade, distribuição e abundância de pequenos mamíferos em uma paisagem silvícultural. A riqueza de espécies e a diversidade de famílias dos pequenos mamíferos tem sido predominantemente determinada pela área porcentual de vegetação nativa. No entanto, a abundância de pequenos mamíferos pode ser determinada por uma estimativa indireta da biomassa da vegetação nativa (e.g., NDVI), que pode ser considerada uma métrica de paisagem 3D, pois está relacionada ao volume. Portanto, para ter sucesso na avaliação do valor da paisagem agrícola, os estudos futuros devem considerar o contexto da paisagem, bem como as métricas da paisagem associadas à análise dos dados geoespaciais e as distintas respostas das espécies.

The recent move to in situ conservation management world-wide is supported by, and stems from the 1992 International Convention on Biological Diversity. The Department of Conservation - charged with the conservation of New Zealand's natural resources - has directed efforts towards the restoration of natural processes as an avenue to halt local biodiversity decline. Ecosystem, habitat, and nature restoration programmes such as the Boundary Stream Mainland Island Project (BSMIP) represent the forefront of conservation management, combining intensive multi-species pest control, with broad-scale hierarchical monitoring programmes. Monitoring programmes confer information that is intended to support decision-making and management by the reduction of uncertainty, or by increasing knowledge. The validity of monitoring programmes depends on three key parts; the guiding objectives, biological relevance, and statistical reliability. Seven major long-term monitoring programmes established at the BSMIP were evaluated according to the above criteria. All monitoring programmes had appropriate guiding objectives, and were biologically relevant (outcome and result monitoring were balanced respective to each other and to the restoration intervention and efforts at BSMIP). The statistical reliability of the programmes was appraised with the use of the Computer programme MONITOR, which provided a calculated value for the statistical power of the monitoring programmes. All monitoring programmes except two (Lizard monitoring: which was initially designed as a short-term species survey, and Mustelid monitoring: which would be a good candidate for a double sampling methodology) had a robust design (evaluated using the actual initial data, and conservative criteria for the detection of population change). The monitoring programmes that did achieve a level of statistical robustness, provided a statistical power of 0.8 ( 80%) within appropriate timeframes for restoration of ecosystem processes (e.g. the timeframe for detection of a 10% change in the abundance, density, relative index, etc of the Result monitoring programmes: Rodents = three years, Possums = six years, and Outcome monitoring programmes: Weta = five years, Ground Invertebrates = four years, Birds (species nos.) = four years, Vegetation (Species, and sapling nos.) = 15 years). The guiding objectives for monitoring programmes must have clear, specific, measurable, and achievable goals, in-order to identify appropriate variables, in both spatial and temporal scales. The biological relevance or "linkage" between monitored groups is important and must be at least outlined, for monitoring programmes to be able to identify potential cause and effect. Statistical reliability (the balance between statistical significance, statistical power, and the timeframe for a conclusive result to be determined) is important, as it is the key method of detecting change. Statistical power can improve the design and efficiency of monitoring programmes and clarify research results. Power analysis has become readily available for researchers and managers with the development of computer programmes specifically designed for this task.

Studies in agricultural landscapes have shown that anthropogenic environments may be relevant to wildlife species. Given the extent of these areas efficient research methods are needed to assess its ecological value in terms of local diversity, such as the use of biological indicators. The main goal here was to evaluate the possible relationship between the native vegetation biomass and diversity of small mammals in a silvicultural landscape of São Paulo. The study was developed at Fazenda Três Lagoas, which is part of the \"Programa de Pesquisa em Biodiversidade\" (PPBio), at Angatuba municipality, State of São Paulo, and lasted nine months. From May 2015 to March 2016 nine sampling campaigns were carried over a grid of 15 pitfall traps, five in Eucalyptus plantations, five in native vegetation and five in abandoned pastures. In the Chapter 1 the distribution and abundance patterns of small mammals on a silvicultural landcape during the early second cycle of Eucalyptus plantation in Southeastern Brazil was evaluated. A total of 672 individuals from 15 species of the orders Rodentia (9 spp.) and Didelphimorphia (6 spp.) were captured and five new species were detected in the study area in comparison to the first cycle. Although these species are predominantly generalists, there were differences in the abundance of small mammals in the three environments. The presence of native vegetation patches associated with riparian areas and abandoned pastures and the role of small mammals as a food resource for predators on a trophic structure, gives a certain conservation value to silvicultural landscapes in southeastern Brazil. In the Chapter 2 the relationship between landscape metrics and patterns of diversity, distribution and abundance of small mammals in a silvicultural landscape were evaluated. The species richness and family diversity of small mammals have been predominantly determined by the percentage of native vegetation. However, the abundance of small mammals can be determined by an indirect estimate of the native vegetation biomass (i.e., NDVI), which can be considered a 3D landscape metric as it is related to volume. Therefore, to succeed in assessing the value of agricultural landscape, future studies should consider landscape context, as well as the landscape metrics associated with geospatial data analysis and the distinct responses of species. / Estudos em paisagens agrícolas têm mostrado que ambientes antrópicos podem ser relevantes para muitas espécies selvagens. Dada a extensão destas áreas, são necessários métodos eficientes de pesquisa para avaliar seu valor ecológico em termos de diversidade local, tais como o uso de indicadores biológicos. O presente estudo teve como objetivo geral avaliar a possível relação entre a biomassa de vegetação nativa e a diversidade de mamíferos de pequeno porte em uma paisagem silvicultural do estado de São Paulo. O estudo foi desenvolvido na Fazenda Três Lagoas, que é parte do Núcleo Angatuba do Programa de Pesquisa em Biodiversidade (PPBio), no município de Angatuba, Estado de São Paulo e teve a duração de nove meses. De maio de 2015 a março de 2016, foram realizadas campanhas mensais de amostragem em uma grade amostral com 15 conjuntos de armadilhas de interceptação e queda (pitfall), sendo cinco nas plantações de Eucalyptus spp., cinco em vegetação nativa e cinco em pasto abandonado. No Capítulo 1 foram avaliados os padrões de distribuição e abundância de pequenos mamíferos em uma paisagem silvicultural ao início do segundo ciclo de plantações de Eucalyptus no Sudeste do Brasil. Um total de 672 indivíduos de 15 espécies das ordens Rodentia (9 spp.) e Didelphimorphia (6 spp.) foram capturados e cinco novas espécies foram detectadas na área de estudo em relação ao primeiro ciclo. Embora as espécies presentes sejam predominantemente generalistas, houve diferença na abundância de pequenos mamíferos nos três ambientes. A presença de fragmentos de vegetação nativa associados a áreas ripícolas e pasto abandonado e o papel dos pequenos mamíferos como recurso alimentar para predadores em uma estrutura trófica, atribui um valor de conservação às paisagens silviculturais no sudeste do Brasil. No Capítulo 2, o objetivo foi avaliar a relação entre métricas da paisagem e padrões de diversidade, distribuição e abundância de pequenos mamíferos em uma paisagem silvícultural. A riqueza de espécies e a diversidade de famílias dos pequenos mamíferos tem sido predominantemente determinada pela área porcentual de vegetação nativa. No entanto, a abundância de pequenos mamíferos pode ser determinada por uma estimativa indireta da biomassa da vegetação nativa (e.g., NDVI), que pode ser considerada uma métrica de paisagem 3D, pois está relacionada ao volume. Portanto, para ter sucesso na avaliação do valor da paisagem agrícola, os estudos futuros devem considerar o contexto da paisagem, bem como as métricas da paisagem associadas à análise dos dados geoespaciais e as distintas respostas das espécies.

La communication par émission sonore est un trait comportemental répandu chez les animaux terrestres. Les riches textures sonores de la forêt neotropicale nous suggèrent que la faune est non seulement abondante, mais aussi diverse et dynamique. Cette facette de la biodiversité peut révéler des informations précieuses sur les communautés animales qui habitent les milieux tropicaux, mais reste largement méconnue. Comment mesurer la diversité acoustique tropicale pour aborder des questions écologiques ? Dans le cadre de l'écoacoustique, nous avons cherché à révéler des structures dissimulées dans le paysage sonore de la forêt neotropicale, et tenter d’expliquer leurs présences à travers les processus écologiques sous-jacents. Tout d’abord, nous avons suivi la dynamique spatio-temporelle d’une empreinte sonore amazonienne, le chant de l’oiseau tropical Lipaugus vociferans, montrant une activité liée à des caractéristiques spécifiques d’habitat. Puis, nous nous sommes intéressés aux communautés d’amphibiens. L’analyse de variables acoustiques et météorologiques nous a permis de mieux comprendre les causes, patrons et conséquences du comportement reproductif explosif. Enfin, nous avons adapté de nouveaux outils de calcul, issus des disciplines de l'apprentissage automatique et de la reconnaissance de formes, pour proposer une analyse efficace, objective et facilement reproductible de grands jeux de données acoustiques. L’écoacoustique, renforcée par des algorithmes informatiques, émerge comme une approche clé pour les programmes de suivis de biodiversité à large échelle, permettant de mieux comprendre et valoriser la diversité de formes de vies unique abritée par la forêt tropicale. / Acoustic signalling is a common behavioural trait among terrestrial animals. The rich sound textures of neotropical forest echo that wildlife is not only abundant, but also diverse and dynamic. This facet of biodiversity can reveal valuable insights of animal communities inhabiting tropical environments, yet remains poorly understood. How to best measure tropical acoustic diversity to address ecological questions? Based on the ecoacoustic framework, we explored the soundscape of neotropical forest, revealing patterns and investigating the ecological underlying processes. First, we tracked the spatiotemporal dynamics of an amazonian soundmark, the song of the bird Lipaugus vociferans, showing activity patterns related to specific habitat features. Then, we investigated amphibian communities with very brief reproduction periods. Coupling acoustic and environmental variables, we shed light on the causes, patterns and consequences of explosive breeding events. Finally, we adapted novel computational tools from the machine learning and pattern recognition disciplines to provide an efficient, objective and replicable analysis of large acoustic datasets. Ecoacoustics, powered with computer algorithms, emerge as a suitable approach to scale-up biodiversity monitoring programs, allowing to better understand and cherish the unique diversity of life sustained by tropical forest.

As the world explores opportunities to develop offshore renewable energy capacity, there will be a growing need for pre-construction biological surveys and post-construction monitoring in the challenging marine environment. Underwater video is a powerful tool to facilitate such surveys, but the interpretation of the imagery is costly and time-consuming. Emerging technologies have improved automated analysis of underwater video, but these technologies are not yet accurate or accessible enough for widespread adoption in the scientific community or industries that might benefit from these tools. To address these challenges, prior research developed a website that allows to: (1) Quickly play and annotate underwater videos, (2) Create a short tracking video for each annotation that shows how an annotated concept moves in time, (3) Verify the accuracy of existing annotations and tracking videos, (4) Create a neural network model from existing annotations, and (5) Automatically annotate unwatched videos using a model that was previously created. It uses both validated and unvalidated annotations and automatically generated annotations from trackings to count the number of Rathbunaster californicus (starfish) and Strongylocentrotus fragilis (sea urchin) with count accuracy of 97% and 99%, respectively, and F1 score accuracy of 0.90 and 0.81, respectively. The thesis explores several improvements to the model above. First, a method to sync JavaScript video frames to a stable Python environment. Second, reinforcement training using marine biology experts and the verification feature. Finally, a hierarchical method that allows the model to combine predictions of related concepts. On average, this method improved the F1 scores from 0.42 to 0.45 (a relative increase of 7%) and count accuracy from 58% to 69% (a relative increase of 19%) for the concepts Umbellula Lindahli and Funiculina.

Thesis: Ph. D., Joint Program in Oceanography/Applied Ocean Science and Engineering (Massachusetts Institute of Technology, Department of Biology; and the Woods Hole Oceanographic Institution), 2014. / This electronic version was submitted by the student author. The certified thesis is available in the Institute Archives and Special Collections. / Cataloged from PDF student-submitted version of thesis. "September 2014." / Includes bibliographical references (pages 191-201). / Synechococcus is a ubiquitous marine primary producer. Our understanding of the factors that determine its abundance has been limited by available observational tools, which have not been able to resolve population dynamics at timescales that match response times of cells (hours-days). Development of an automated flow cytometer (FlowCytobot) has enabled hourly observation of Synechococcus at the Martha's Vineyard Coastal Observatory (MVCO) since 2003. In order to ascribe changes in cell abundances to either growth or loss processes, information on division rate is needed. I refined a matrix population model that relates diel changes in the distribution of cell volume to division rate and demonstrated that it provides accurate estimates of daily division rate for both cultured and natural populations. Application of the model to the 11-year MVCO time series reveals that division rate is temperature limited during winter and spring, but light limited during fall. Inferred loss rates closely follow division rate in magnitude over the entire seasonal cycle, suggesting that losses are mainly generated by biological processes. While Synechococcus cell abundance, division rate, and loss rate demonstrate striking seasonal patterns, there are also significant shorter timescale variations and important multi-year trends that may be linked to climate. Interpretation of population dynamic patterns is complicated by the diversity found within marine Synechococcus, which is partitioned into 20 genetically distinct clades. Each clade may represent an ecotype, with a distinct ecological niche. To understand how diversity may affect population dynamics, I assessed the diversity at MVCO over annual cycles with culture-independent and dependent approaches. The population at MVCO is diverse, but dominated by clade I representatives throughout the year. Other clades were only found during summer and fall. High through-put sequencing of a diversity marker allowed a more quantitative investigation into these patterns. Five main Synechococcus oligotypes that comprise the population showed seasonal abundance patterns: peaking either during the spring bloom or during late summer and fall. This pattern strongly suggests that features of seasonal abundance are affected by the underlying diversity structure. Synechococcus abundance patterns result from a complex interplay among seasonal environmental changes, diversity, and biological losses. / by Kristen Rachell Hunter-Cevera. / Ph. D.