Classification and ranking of environmental recordings to facilitate efficient bird surveys

This thesis contributes novel computer-assisted techniques to facilitating bird species surveys from a large number of environmental audio recordings. These techniques are applicable to both manual and automated recognition of bird species by removing irrelevant audio data and prioritising those relevant data for efficient bird species detection. This work also represents a significant step towards using automated techniques to support experts and the general public to explore and gain a better understanding of vocal species

Acoustic indices as proxies for biodiversity: a meta-analysis

As biodiversity decreases worldwide, the development of effective techniques to track changes in ecological communities becomes an urgent challenge. Together with other emerging methods in ecology, acoustic indices are increasingly being used as novel tools for rapid biodiversity assessment. These indices are based on mathematical formulae that summarise the acoustic features of audio samples, with the aim of extracting meaningful ecological information from soundscapes. However, the application of this automated method has revealed conflicting results across the literature, with conceptual and empirical controversies regarding its primary assumption: a correlation between acoustic and biological diversity. After more than a decade of research, we still lack a statistically informed synthesis of the power of acoustic indices that elucidates whether they effectively function as proxies for biological diversity. Here, we reviewed studies testing the relationship between diversity metrics (species abundance, species richness, species diversity, abundance of sounds, and diversity of sounds) and the 11 most commonly used acoustic indices. From 34 studies, we extracted 364 effect sizes that quantified the magnitude of the direct link between acoustic and biological estimates and conducted a meta-analysis. Overall, acoustic indices had a moderate positive relationship with the diversity metrics (r = 0.33, CI [0.23, 0.43]), and showed an inconsistent performance, with highly variable effect sizes both within and among studies. Over time, studies have been increasingly disregarding the validation of the acoustic estimates and those examining this link have been progressively reporting smaller effect sizes. Some of the studied indices [acoustic entropy index (H), normalised difference soundscape index (NDSI), and acoustic complexity index (ACI)] performed better in retrieving biological information, with abundance of sounds (number of sounds from identified or unidentified species) being the best estimated diversity facet of local communities. We found no effect of the type of monitored environment (terrestrial versus aquatic) and the procedure for extracting biological information (acoustic versus non-acoustic) on the performance of acoustic indices, suggesting certain potential to generalise their application across research contexts. We also identified common statistical issues and knowledge gaps that remain to be addressed in future research, such as a high rate of pseudoreplication and multiple unexplored combinations of metrics, taxa, and regions. Our findings confirm the limitations of acoustic indices to efficiently quantify alpha biodiversity and highlight that caution is necessary when using them as surrogates of diversity metrics, especially if employed as single predictors. Although these tools are able partially to capture changes in diversity metrics, endorsing to some extent the rationale behind acoustic indices and suggesting them as promising bases for future developments, they are far from being direct proxies for biodiversity. To guide more efficient use and future research, we review their principal theoretical and practical shortcomings, as well as prospects and challenges of acoustic indices in biodiversity assessment. Altogether, we provide the first comprehensive and statistically based overview on the relation between acoustic indices and biodiversity and pave the way for a more standardised and informed application for biodiversity monitoringThis study was supported by a research project funded by the Comunidad de Madrid and the European Social Fund (PEJ2018-AI/AMB-9957, to D. L.). We thank Camille Desjonquères for her valuable comments on the study design, Alison Cooper for her exhaustive and insightful revision of the manuscript, and anonymous reviewers for their significant contribution. I. A. and L. S. M. S. acknowledge research grants provided by the Comunidad de Madrid (PEJ-2018-AI/ AMB-9957, to D. L.) and the Ministerio de Economía, Industria y Competitividad of Spain (PEJ-2018-004603-A, to D. L.), respectively, together with the support of the European Social Fund. H. L. was supported by the FPI program of the Ministerio de Ciencia e Innovacion of Spain (grant CGL2017-86926-P). D. L. also acknowledges a postdoctoral grant provided by the Comunidad de Madrid (2020-T1/AMB-20636, Atraccion de Talento Investigador, Spain) and a research project funded by the Ministerio de Economía, Industria y Competitividad (CGL2017-88764-R, MINECO/AEI/FEDER, Spain

Avian responses to fire regimes in montane dry sclerophyll forests of south-eastern Australia

Wildfires are becoming larger and more frequent in forests under climate change, with corresponding increases in area burnt recently and at high-severity. Australian fire regimes are changing rapidly, but the implications for fauna are poorly understood. The first of two overarching aims of this research was to increase understanding of the mechanisms and processes that underpin avian responses to fire regimes in montane dry sclerophyll forests of south-eastern Australia. The second was to investigate the implications of altered fire regimes for birds through evaluation of their responses where fire activity is currently high

Science-based restoration monitoring of coastal habitats, Volume Two: Tools for monitoring coastal habitats

Healthy coastal habitats are not only important ecologically; they also support healthy coastal communities and improve the quality of people’s lives. Despite their many benefits and values, coastal habitats have been systematically modified, degraded, and destroyed throughout the United States and its protectorates beginning with European colonization in the 1600’s (Dahl 1990). As a result, many coastal habitats around the United States are in desperate need of restoration. The monitoring of restoration projects, the focus of this document, is necessary to ensure that restoration efforts are successful, to further the science, and to increase the efficiency of future restoration efforts

Investigating Spatiotemporal Distribution and Habitat use of Poorly Understood Procellariiform Seabirds on a Remote Island in American Samoa.

Ph.D. Thesis. University of Hawaiʻi at Mānoa 2017

Zooplankton seasonality at high latitudes: From community to behaviour

This thesis describes the seasonality of the mesozooplankton community in Ramfjord, a shallow high-latitude fjord, in terms of diversity and behavior, using a combination of new and traditional methods. The approach aimed to gain insight into how environmental drivers such as photoperiod and food availability shape seasonal changes in mesozooplankton community structure and Calanus spp. behavior. Seasonal changes in diel vertical migration (DVM) were closely linked to the seasonal changes in day length. Monthly sampling over an entire annual cycle revealed that Ramfjord has particular characteristics such as the dominance of small copepods year-round in terms of abundance and biomass and a population of Calanus finmarchicus that enters a winter resting state rather than a diapause stage. This investigation also used metabarcoding as a quantitative tool for the first time, demonstrating the usefulness of this method in establishing the mesozooplankton community structure. Monthly monitoring of Calanus spp. swimming activity with the locomotor activity method confirmed the efficiency of this method in detecting overwintering in the Calanus population and determined that swimming activity can be used as a proxy for DVM behavior. This thesis demonstrates that the combination of newly developed methods (locomotor activity monitor and metabarcoding as a quantitative tool) with more traditional methods, such as visual identification and active acoustics, can provide new understanding of seasonal changes in the mesozooplankton community structure and behavior

The avian dawn chorus across Great Britain: using new technology to study breeding bird song

The avian dawn chorus is a period of high song output performed daily around sunrise during the breeding season. Singing at dawn is of such significance to birds that they remain motivated to do so amid the noise of numerous others. Yet, we still do not fully understand why the dawn chorus exists. Technological advances in recording equipment, data storage and sound analysis tools now enable collection and scrutiny of large acoustic datasets, encouraging research on sound-producing organisms and promoting ‘the soundscape’ as an indicator of ecosystem health. Using an unrivalled dataset of dawn chorus recordings collected during this thesis, I explore the chorus throughout Great Britain with the prospect of furthering our understanding and appreciation of this daily event. I first evaluate the performance of four automated signal recognition tools (‘recognisers’) when identifying the singing events of target species during the dawn chorus, and devise a new ensemble approach that improves detection of singing events significantly over each of the recognisers in isolation. I then examine daily variation in the timing and peak of the chorus across the country in response to minimum overnight temperature. I conclude that cooler temperatures result in later chorus onset and peak the following dawn, but that the magnitude of this effect is greater at higher latitude sites with cooler and less variable overnight temperature regimes. Next, I present evidence of competition for acoustic space during the dawn chorus between migratory and resident species possessing similar song traits, and infer that this may lead either to fine-scale temporal partitioning of song, such that each competitor maintains optimal output, or to one competitor yielding. Finally, I investigate day-to-day attenuation of song during the leaf-out period from budburst through to full-leaf in woodland trees, and establish the potential for climate-driven advances in leaf-out phenology to attenuate song if seasonal singing activity in birds has not advanced to the same degree. I find that gradual attenuation of sound through the leaf-out process is dependent on the height of the receiver, and surmise that current advances in leaf-out phenology are unlikely to have undue effect on song propagation. This project illustrates the advantage of applying new technology to ecological studies of complex acoustic environments, and highlights areas in need of improvement, which is essential if we are to comprehend and preserve our natural soundscapes

Smallholder vanilla agroforestry in Madagascar: biodiversity, ecosystem services and yields in a land-use context

Änderungen der Landnutzung bedrohen weltweit die Artenvielfalt und Ökosystemdienstleistungen. Tropische Regionen sind heute davon besonders betroffen: natürliche Ökosysteme werden zu großflächigen Monokulturen oder zu kleinräumigen Mosaiklandschaften, letztere geprägt von kleinbäuerlicher Landwirtschaft. In beiden Fällen lassen sich durch die Umwandlung natürlicher Ökosysteme in landwirtschaftlich genutzte Flächen die Erträge zumindest kurzfristig stark vergrößern. In Nordost-Madagaskar findet zurzeit ein rapider Landnutzungswandel statt, getrieben durch Anbau von Reis durch Brandrodung sowie die Umwandlung von Wäldern und Brachflächen in Vanille-Agroforste. Das Resultat dieser Prozesse ist eine kleinräumige, von Kleinbauern bewirtschaftete, sehr heterogene Kulturlandschaft. Diese Dissertation zeigt, was dieser Landnutzungswandel für die Biodiversität und Ökosystemdienstleistungen bedeutet, wie Ernteerträge und Profitabilität Landnutzungsentscheidungen beeinflussen, und wo sich in Nordost-Madagaskar Chancen für den Naturschutz bieten. Damit ist die Arbeit ein Beitrag zum noch jungen Forschungsfeld der Landnutzungsforschung in Madagaskar. Dass dieses Thema noch wenig untersucht wurde, zeigt sich auch darin, dass bis anhin fast nichts über Artenvielfalt und Ökosystemdienstleistungen in Vanille-Agroforsten bekannt ist. Um die verschiedenen Formen der Landnutzung vergleichen zu können, haben wir 80 Flächen in zehn Dörfern und im Marojejy Nationalpark ausgewählt. Auf diesen Flächen haben wir den Großteil der Daten zu Biodiversität und Ökosystemdienstleistungen gesammelt, die als Grundlage für diese Arbeit dienen. Im Fokus standen sieben Landnutzungstypen: Primärwald, Waldfragment, Vanille-Agroforst mit Waldursprung, Vanille-Agroforst mit Brachlandursprung, krautige Brache, holzige Brache, und Naßreis. Um genauere Daten über Baumdynamik und Ernten in Vanille-Agroforsten zu sammeln, habe wir zusätzlich eine Chronosequenz mit 209 Vanille-Agroforsten erforscht. Ferner enthält diese Dissertation ei-nen Review zur Landnutzungsgeschichte in Agroforstsystemen (Kapitel 2). Die Resultate zeigen unter anderem, dass sich Artengemeinschaften von Vögeln (Kapitel 3 & 4), Reptilien, und Amphibien (Kapitel 5) stark zwischen verschiedenen Landnutzungstypen unterscheiden und dass Primärwald unersetzlich für viele Arten ist, insbesondere die endemischen. Vanille-Agroforstsysteme bieten Chancen für den Naturschutz, insbesondere wenn diese auf Brachland und nicht im Wald etabliert werden (Kapitel 3 - 9). Zudem sind Vanilleernten in Agroforstsystemen unabhängig vom Beschattungsgrad. Der Anbau von Vanille in baumreichen Agroforsten ist demnach ohne Ernteverlust realisierbar (Kapitel 7 & 8) und hat Vorteile für Biodiversität und Ökosystemdienstleistungen. Die vorliegende Dissertation führt zu einer wesentlichen Verbesserung unseres Verständnisses bezüglich des Wandels der Artenvielfalt und der Ökosystemleistungen in der kleinbäuerlich geprägten Agrarlandschaft des nordöstlichen Madagaskars. Sie gibt auch erste Einblicke in den Einfluss von Landnutzungsgeschichte, Schattenbäumen und Bewirtschaftungspraktiken auf Vanilleernten. Das Herausheben der Bedeutung der Landnutzungsgeschichte für Biodiversität und Ökosystemleistungen in tropischen Agroforstsystemen stellt zudem eine konzeptionelle Weiterentwicklung des Forschungsfeldes dar.Land-use change threatens biodiversity and ecosystem services worldwide. Tropical areas are currently particularly affected: natural ecosystems are being transformed into large-scale monocultures or small-scale mosaic landscapes characterized by smallholder agriculture. In both cases, the conversion of natural ecosystems into agriculturally used areas can greatly increase yield, at least in the short term. A rapid change in land use is currently taking place in north-eastern Madagascar, driven by two main factors: the cultivation of rice through shifting cultivation and the conversion of forests and fallow land into vanilla agroforestry. The result of these processes is a small-scale and very heterogeneous agricultural landscape. This dissertation shows what this land-use change means for biodiversity and ecosystem services, how realized harvests and profitability influence land use decisions, and where there are opportunities for nature con-servation through targeted policy interventions in north-eastern Madagascar. Importantly, this is a greatly under-researched topic, given that research on the conservation value of converted lands in Madagascar is still in its infancy. Indeed, nearly nothing has been pub-lished on biodiversity, ecosystem services, and yields in vanilla agroforests. To compare different forms of land use, we selected 80 plots in 10 villages and in Marojejy National Park where we collected a large part of the biodiversity and ecosystem service data that underpins this dissertation. The seven land-use types were old-growth forest, forest fragment, forest-derived vanilla agroforestry, fallow-derived vanilla agroforestry, herba-ceous fallow, woody fallow, and rice paddy. To obtain more precise data on tree dynamics and harvests in vanilla agroforests, we additionally researched a chronosequence with 209 vanilla agroforests. Furthermore, this thesis also contains a review on the importance of considering land-use history for biodiversity and ecosystem services in agroforestry sys-tems (Chapter 2). There are three principal findings: firstly, species communities of birds (Chapters 3 & 4), reptiles and amphibians (Chapter 5) differ greatly between land-use types and that old-growth forest is irreplaceable for many species, especially the endemic ones. Secondly, vanilla agroforestry systems offer conservation opportunities, especially if established on fal-low land instead of inside forest (Chapters 3 - 9). Thirdly, vanilla harvests in agroforestry systems are independent of canopy cover, making vanilla cultivation in tree-rich agroforests feasible, thereby reaping the associated benefits for biodiversity and ecosystem ser-vices without yield costs (Chapters 7 & 8). This dissertation thus provides a major advancement of our understanding of biodiversity change and ecosystem services in the agricultural smallholder landscape of north-eastern Madagascar. It also sheds some first light on the complex interplay between land-use history, shade trees, and management practices in determining vanilla yields in vanilla agroforests. Lastly, this thesis also provides a conceptual advancement of the field, by identifying the importance of land-use history in determining biodiversity and ecosystem services in tropical agroforests.2021-08-1