Avian communities and ecoacoustics in a tropical human-modified landscape

Large areas of the tropics have been cleared of forest and converted to agriculture. The consequent human-modified landscapes (HMLs) comprise a heterogenous mix of habitats; forest fragments and riparian strips are embedded in a matrix of cattle pasture, non-native timber plantations, and urban centres. These habitat changes can have dramatic consequences for wildlife, leading to range shifts and extirpations. In turn, this can influence the integrity of ecosystem services such as frugivory and seed dispersal. Understanding how habitat conversion affects natural ecosystems is critical to inform conservation interventions, but requires long-term biodiversity monitoring and detailed knowledge of species-level responses to HMLs. The research presented in this thesis was conducted in the Emparador HML, in central Republic of Panama. In Chapter 2, we show that the regional avian community is shaped by extent of forest cover across the landscape, and to a lesser degree, extent of forest fragmentation and distance to core forest. Effects of forest cover and fragmentation were examined at local (10 ha) and landscape (500 ha) scales. Species-level responses to these factors varied widely; while abundance of many species increased with greater local-scale forest cover, greater landscape-scale forest cover was often associated with declines. Generalist species that readily persist in HMLs still responded positively to local-scale forest cover, suggesting that even smaller forest fragments in these landscapes are important for maintaining diverse avian assemblages. Critically, we found that species’ responses were not associated with particular traits such as dietary composition or forest dependence, highlighting that species may often exhibit idiosyncratic responses to landscape structure. Chapters 3 and 4 address the wider issue of long-term monitoring, and the potential for data collection over large spatiotemporal scales using remote audio recorders. Ecoacoustics, the study of environmental sound is a relatively new discipline, and as such there is still considerable uncertainty surrounding best-practice for collecting and processing recordings. One of the most straightforward means of utilising audio recordings for environmental monitoring is via acoustic indices. These are objective measures of sound based on features such as pitch and amplitude. To date, attempts to use these indices have been hindered by inconsistent or inappropriate methodologies. In Chapter 3, we determine how many recordings are required to comprehensively capture a soundscape, the acoustic energy of a location. Furthermore, we demonstrate that there are habitat-specific patterns in acoustic indices values, suggesting that these indices reflect differences in vegetation structure and wildlife. We develop this further in Chapter 4, where we show that avian species richness and abundance are clearly linked to patterns in acoustic indices values. Critically, these patterns were coherent among habitat types emphasising their potential for monitoring. Acoustic indices sensitive to the frequencies occupied by bird song have the greatest potential for monitoring an avian community. The results from these two chapters suggest that acoustic indices can be effective tools for monitoring biodiversity, with values reflecting consistent differences across habitats, and among avian assemblages. Audio recordings are a source of permanent, verifiable evidence that can be collected at much greater spatiotemporal scales than traditional biodiversity monitoring data. As the use of audio recorders grows, it is important to compare their efficacy with standard methods of data collection. In Chapter 5, we contrast data derived from audio recordings with that gathered using standard point count methods, and consider whether recorders are a feasible means of surveying antbirds (Thamnophilidae), a disturbance-sensitive avian taxon. Both approaches revealed species’ responses to landscape structure, with qualitatively similar patterns in response to forest cover and vegetation quality. We show that common species can be readily monitored using audio recorders, with greater levels of detectability compared with point counts. However, rarer species were more likely to be detected using point counts. The work presented in this thesis helps to explain the patterns seen in avian responses to Neotropical HMLs. In particular we emphasise the importance of forest cover for maintaining bird assemblages in these landscapes. We demonstrate the utility of audio recorders for data collection, and highlight their potential for future biodiversity monitoring. In the face of human population growth, and ongoing habitat disturbance and agricultural intensification, conservation efforts are essential to avoid widespread species extinctions and ecosystem collapse. Interventions must take place in HMLs, to bolster ecosystem services, provide buffer zones for protected areas, and improve connectivity in the wider landscape

Species-specific responses to landscape fragmentation: implications for management strategies

Habitat fragmentation affects the integrity of many species, but little is known about species-specific sensitivity to fragmentation. Here, we compared the genetic structure of four freshwater fish species differing in their body size (Leuciscus cephalus; Leuciscus leuciscus; Gobio gobio and Phoxinus phoxinus) between a fragmented and a continuous landscape. We tested if, overall, fragmentation affected the genetic structure of these fish species, and if these species differed in their sensitivity to fragmentation. Fragmentation negatively affected the genetic structure of these species. Indeed, irrespective of the species identity, allelic richness and heterozygosity were lower, and population divergence was higher in the fragmented than in the continuous landscape. This response to fragmentation was highly species-specific, with the smallest fish species (P. phoxinus) being slightly affected by fragmentation. On the contrary, fish species of intermediate body size (L. leuciscus and G. gobio) were highly affected, whereas the largest fish species (L. cephalus) was intermediately affected by fragmentation. We discuss the relative role of dispersal ability and effective population size on the responses to fragmentation we report here. The weirs studied here are of considerable historical importance. We therefore conclude that restoration programmes will need to consider both this societal context and the biological characteristics of the species sharing this ecosyste

Optimising habitat creation for woodland birds: the relative importance of local vs landscape scales

Global land-use change and industrialisation has driven biodiversity declines and impaired ecosystem functioning. Recently, there have been large-scale efforts to not only halt habitat loss but create and restore habitat on formerly managed (e.g. agricultural) land. However, although the effects of habitat loss and fragmentation on biodiversity are well understood, our understanding of how biodiversity responds to habitat created in a patchy configuration is not. In particular, little is known about the relative importance of local (e.g. patch size) vs landscape scales (e.g. amount of habitat in the landscape) for restoring biodiversity in created habitat. Here, a long-term, large-scale natural experiment (the Woodland Creation and Ecological Networks project) was used to understand how bird species, communities and behaviour respond to woodland created in a patchy configuration on post-agricultural land. I used a combination of direct and indirect survey methods to quantify bird diversity, abundance and vocal behaviour in post-agricultural woodlands of known age in Great Britain. I show that secondary woodlands favour generalist species and older patches contain more individuals and species due to their vegetation structure. In relative terms, local-scale factors such as patch size made the greatest contribution to bird diversity and abundance. Colonisation events drive community assembly in new habitat, and I found that large-scale (km2) habitat patterns were more important than patch-level factors during colonisation of breeding territories by a long distance migrant bird (Willow Warbler Phylloscopus trochilus). Land management practices surrounding a habitat patch can also affect its perceived quality and relative attractiveness to potential colonisers. Using the Eurasian Wren Troglodytes troglodytes as a model species, I found that high proportions of agricultural land at woodland edges caused an increase in perceived predation risk. In conclusion, I suggest that post-agricultural woodlands rapidly provide valuable habitat for generalist woodland birds. Local, patch-level factors (area, vegetation structure) also appear relatively more important than landscape factors for woodland bird communities. Land-managers seeking to maximise the benefits of woodland creation for birds should thus focus on creating large patches with a diverse vegetation structure

Impacts of coffee fragmented landscapes on biodiversity and microclimate with emerging monitoring technologies

Habitat fragmentation and loss are causing biodiversity declines across the globe. As biodiversity is unevenly distributed, with many hotspots located in the tropics, conserving and protecting these areas is important to preserve as many species as possible. Chapter 2 presents an overview of the Ecology of the Atlantic Forest, a highly fragmented biodiversity hotspot. A major driver of habitat fragmentation is agriculture, and in the tropics coffee is major cash crop. Developing methods to monitor biodiversity effectively without labour intensive surveys can help us understand how communities are using fragmented landscapes and better inform management practices that promote biodiversity. Acoustic monitoring offers a promising set of tools to remotely monitor biodiversity. Developments in machine learning offer automatic species detection and classification in certain taxa. Chapters 3 and 4 use acoustic monitoring surveys conducted on fragmented landscapes in the Atlantic Forest to quantify bird and bat communities in forest and coffee matrix, respectively. Chapter 3 shows that acoustic composition can reflect local avian communities. Chapter 4 applies a convolutional neural network (CNN) optimised on UK bat calls to a Brazilian bat dataset to estimate bat diversity and show how bats preferentially use coffee habitats. In addition to monitoring biodiversity, monitoring microclimate forms a key part of climate smart agriculture for climate change mitigation. Coffee agriculture is limited to the tropics, overlapping with biodiverse regions, but is threatened by climate change. This presents a challenge to countries strongly reliant on coffee exports such as Brazil and Nicaragua. Chapter 5 uses data from microclimate weather stations in Nicaragua to demonstrate that sun-coffee management is vulnerable to supraoptimal temperature exposure regardless of local forest cover or elevation.Open Acces

Habitat Features and Behavioral Plasticity Promote Barred Owl Presence in Developed Landscapes

Despite extensive accounts in the literature describing Barred Owls (Strix varia) as obligate forest-interior species that are sensitive to development, Barred Owls have increasingly been found in urbanized landscapes. Due to the limited number of studies on Barred Owls within the context of development, our understanding of the processes that facilitate Barred Owls within anthropogenic landscapes is limited. In the Piedmont region of the southeastern United States, South Carolina, the presence of Barred Owls in suburbs and small-town centers precipitated our research team to examine which habitat features facilitate their occurrence near development. We conducted surveys using callbacks and autonomous recording units within a 300 km2 region centered around Clemson, South Carolina. We used detection/nondetection data to model the influence of habitat features on Barred Owl occupancy along a development gradient. Tree height was the best predictor of Barred Owl occupancy, regardless of forest coverage. We did not find Barred Owl occupancy to decline with increasing impervious surface density. To further investigate habitat selection at a finer scale, we deployed GPS transmitters on 20 breeding Barred Owls in our region during a single breeding season. We selected territories containing a variety of development density and habitat types to examine predictors of home range size and habitat selection along an urban-rural gradient. We related nocturnal (foraging) locations to habitat features using resource selection functions (RSFs). We explored differential use along a development gradient by modeling interactions between habitat parameters and measures of development in the home range. After accounting for variation attributable to sex, we found that Barred Owl home ranges expanded significantly in size with increasing forest fragmentation in the landscape. Tree height was one of the most important habitat predictors of foraging selection among the variables we evaluated, thus mature urban canopy could be the key to Barred Owl presence in developed landscapes. Barred Owls exhibited differential use based on development in the home range; owls within zones of higher fragmentation had stronger selection for anthropogenic features, such as roads and forest edges. Although our findings confirm that certain habitat features, such as tall canopy, are integral to supporting a breeding population of Barred Owls within development, our results also demonstrate the plasticity of a forest predator previously described as sensitive to urbanization. The presence of Barred Owls in developed landscapes suggests that retaining key habitat features can promote multi-trophic communities even when other aspects of the habitat are highly altered

Bioacoustic monitoring of bird communities and behaviour in fragmented and regenerating tropical dry forests

Vocalizations provide important information about how animals respond to changes in their environments. In this thesis, I use bioacoustic tools to investigate how birds respond to habitat restoration and fragmentation in tropical dry forests of Costa Rica. Tropical dry forests are one of the most imperilled ecosystems in the world, and my study site, the Área de Conservación Guanacaste, is home to the largest remaining stand of this unique ecosystem. In both chapters of this thesis, I collected recordings of bird vocalizations to study avian responses to changes in the Área de Conservación Guanacaste. In my first data chapter, I used passive acoustic monitoring and point-count surveys to measure bird community responses to tropical dry forest regeneration. I found that bird diversity and abundance increase as regenerating forests increase in age. I also found that bird communities become more similar to primary forests with increasing forest succession. My research provides evidence that restoration efforts in northwestern Costa Rica are encouraging the recovery of bird communities. In my second data chapter, I used bioacoustic monitoring to study female and male vocal behaviours in Rufous-and-white Wrens living in fragmented mature forests, with a focus on the influence of neighbours, time of day, and time of year. I found that female wrens changed song types more often with more neighbours, however, I did not observe any effect of neighbours on vocal behaviours in male wrens or on duetting behaviours in both sexes. I found changes in vocal behaviour of female and male wrens in response to time of day and time of year corroborating previous findings. My research contributes to two areas of bird conservation research that require more attention: long-term monitoring of bird communities in changing landscapes, and behavioural monitoring of birds for conservation purposes. Understanding how birds respond to changes in their environment can help guide conservation practices to ensure the continued persistence of healthy bird communities and populations

River Architect

© 2020 The Authors River design is often conceptually approached aiming at either physical channel stability or ecological functionality. We present a novel concept within an open-source software called River Architect that addresses both these goals and estimates costs. River Architect is flexible for site- and application-specific characteristics, with modules for the analysis and design of habitat-enhancing and channel-stabilising feature groups. Ecological assets are assessed as a function of a novel metric that incorporates the seasonal and discharge-dependent preferred habitat area of target species. Calculations of cost estimates and ecological efficiency are illustrated by an example in a gravel-cobble-bed river

Genetic and morphological variation of butterflies in relict habitats

Habitat fragmentation and loss are leading threats to global biodiversity and can alter patterns of dispersal, population dynamics, and genetics with implications for long-term species persistence. Most habitat fragmentation research has focused on recently fragmented species that historically occupied interconnected habitat patches. We know comparatively little about how naturally fragmented species may respond to habitat loss. For these species, local habitat patch quality may influence the dynamics and genetics of populations more than the structure of the surrounding landscape (e.g., degree of isolation of suitable habitat). I examined aspects of the ecology and evolution of populations inhabiting fragmented landscapes, using two butterfly species representing relict populations that are 1) recently fragmented by anthropogenic activities (Mormon metalmark, Apodemia mormo), and 2) naturally fragmented (bog copper, Lycaena epixanthe). I assessed patterns of genetic (amplified fragment length polymorphism, AFLP) and flight-related morphological variation, and their relationship to measures of surrounding landscape structure and local habitat quality. Population genetic analysis of the anthropogenically fragmented Mormon metalmark revealed a high degree of spatial genetic structure, indicating limited gene flow, despite a small geographic scale (\u3c20 \u3ekm). Management of this endangered population should focus on increasing connectivity among the most isolated sub-populations and through urban areas. For the naturally fragmented bog copper, genetic diversity was explained by variables related to patch quality rather than landscape structure. Movement ability in the bog copper (inferred by flight morphology) appeared to depend on both local habitat conditions and the surrounding landscape. Also, using an AFLP-based genome scan approach, I identified signatures of selection in the bog copper associated with fine-scale landscape heterogeneity. My work on the bog copper highlights the importance of considering the effects of local habitat conditions, in addition to habitat isolation, for conservation of fragmented populations. Finally, I also reviewed the current literature (470 articles) to evaluate the quality of AFLP data used in ecological and evolutionary research. I discovered a pervasive lack of consistency and transparency in both the methods used to assess data reproducibility, and in the details of methodology presented. This work has identified an important publishing gap in molecular ecology research

Exploring the uses and value of invertebrate DNA metabarcoding

This thesis reviews and explores the use of DNA metabarcoding techniques on invertebrates, moving beyond biodiversity audits to improve monitoring capabilities in terrestrial ecosystems. Here, metabarcoding is used to look at fine scale differences in arthropod biodiversity, foraging behaviour of native bees, and even to track vertebrate populations. This body of work demonstrates the immense value of this technique to monitor how whole ecosystems respond to change