Varied diversification patterns and distinct demographic trajectories in Ethiopian montane forest bird (Aves: Passeriformes) populations separated by the Great Rift Valley

Taxon-specific characteristics and extrinsic climatic and geological forces may both shape population differentiation and speciation. In geographically and taxonomically focused investigations, differentiation may occur synchronously as species respond to the same external conditions. Conversely, when evolution is investigated in taxa with largely varying traits, population differentiation and speciation is complex and shaped by interactions of Earth’s template and species-specific traits. As such, it is important to characterize evolutionary histories broadly across the tree of life, especially in geographic regions that are exceptionally diverse and under pressures from human activities such as in biodiversity hotspots. Here, using whole-genome sequencing data, we characterize genomic variation in populations of six Ethiopian Highlands forest bird species separated by a lowland biogeographic barrier, the Great Rift Valley (GRV). In all six species, populations on either side of the GRV exhibited significant but varying levels of genetic differentiation. Species’ dispersal ability was negatively correlated with levels of population differentiation. Isolation with migration models indicated varied patterns of population differentiation and connectivity among populations of the focal species. We found that demographic histories—estimated for each individual—varied by both species and population but were consistent between individuals of the same species and sampling region. We found that genomic diversity varied by half an order of magnitude across species, and that this variation could largely be explained by the harmonic mean of effective population size over the past 200,000 years. Overall, we found that even in highly dispersive species like birds, the GRV acts as a substantial biogeographic barrier.

Composition, richness and nestedness of gallery forest bird assemblages in an Amazonian savanna landscape: lessons for conservation

Gallery forests are important to the maintenance of a substantial portion of the biodiversity in neotropical savanna regions, but management guidelines specific to this forest type are limited. Here, we use birds as study group to assess if: (1) functional traits can predict the abundance and occupancy of forest species within a savanna landscape, (2) habitat structures influence the taxonomic, functional, and phylogenetic diversity of forest assemblages, and (3) less diverse gallery forest assemblages are a nested subset of more diverse assemblages living near continuous forests. Then, we propose strategies on how gallery forests can be managed to maintain their species assemblages amidst the fast expansion of human activities across tropical savanna landscapes. We studied 26 sites of gallery forests in an Amazonian savanna landscape and found that: (1) habitat specificity is the only functional trait that predicts species abundance and occupancy across a landscape; (2) phylogenetic diversity is negatively correlated with understory foliage density; (3) the percentage of forests and savannas around sites is positively correlated with both phylogenetic and functional diversity; (4) increasing human activities around gallery forest negatively influences taxonomic and functional diversity; and (5) forest bird assemblages are not distributed at random across the landscape but show a nested pattern caused by selective colonization mediated by habitat filtering. Our combined findings have three implications for the design of conservation strategies for gallery forest bird assemblages. First, maintaining the connectivity between gallery forests and adjacent continuous forests is essential because gallery forest bird assemblages are derived from continuous forest species assemblages. Second, because most species use the savanna matrix to move across the landscape, effectively managing the savanna matrices where gallery forests are embedded is as important to maintaining viable populations of forest bird species as managing the gallery forest themselves. Third, in savanna landscapes planned to be used for agriculture production, protecting gallery forests alone is not enough. Instead, gallery forests should be protected with surrounding savanna buffers to avoid the detrimental effects (edge effects and isolation) of human activities on their biodiversity.

The responses of New Zealand's arboreal forest birds to invasive mammal control

<p>Introduced mammalian predators are responsible for over half of contemporary extinctions and declines of birds. Endemic bird species on islands are particularly vulnerable to invasions of mammalian predators. The native bird species that remain in New Zealand forests continue to be threatened by predation from invasive mammals, with brushtail possums (Trichosurus vulpecula) ship rats (Rattus rattus) and stoats (Mustela erminea) identified as the primary agents responsible for their ongoing decline. Extensive efforts to suppress these pests across New Zealand’s forests have created "management experiments" with potential to provide insights into the ecological forces structuring forest bird communities. To understand the effects of invasive mammals on birds, I studied responses of New Zealand bird species at different temporal and spatial scales to different intensities of control and residual densities of mammals. In my first empirical chapter (Chapter 2), I present two meta-analyses of bird responses to invasive mammal control. I collate data from biodiversity projects across New Zealand where long-term monitoring of arboreal bird species was undertaken. The projects cover a range of treatments including fenced sanctuaries, offshore islands, forests treated periodically and sites lacking significant mammal control. I found that New Zealand bird species exhibit complex responses to the varied and sustained management effort that has occurred across New Zealand’s landscape in the last fifty years. Some species show significant positive outcomes to control, notably the larger endemic species, while others, including highly endemic species, consistently decline after control. In Chapter 3, I estimate the responses of bird populations in the central New Zealand region to changes in ship rat densities. I collaborated with scientists from the Department of Conservation (DOC) and Greater Wellington Regional Council and collated biodiversity data from four restoration projects located across the central New Zealand region. I constructed multiple density impact functions (DIFs), where the effect of a change in density of a pest on a valued resource is quantified, to describe the impacts of ship rat population dynamics on native bird populations. These responses were then modelled in a meta-analysis to provide overall effects for bird populations when rat abundance increases. I identified two taxa that exhibit significant negative responses across the region: the native parakeet species (Cyanoramphus spp.) and the tomtit (Petroica macrocephala). Evidence from single projects also showed that two other species were negatively affected by increases in rats: the South Island kaka (Nestor meridionalis) and the North Island rifleman (Acanthisitta chloris). Conversely, populations of the recently introduced silvereye (Zosterops lateralis) were resilient to rat population recovery as silvereye counts significantly increased the year after an increase in ship rat populations was observed. In Chapter 4, I monitored bird species through a 1080 mammal-control operation in the southern Wairarapa. This operation coincided with a heavy beech mast, an irruptive event that occurs every 2-6 years. Most likely because of the abundance of seed, suppression of ship rats and possums appeared to be short-lived, and detections of these two mammals returned to pre-control levels within one and two years, respectively. Short-term responses of native birds to the control operation were positive: initially, for the small-medium sized bird species (i.e. the bellbird (Anthornis melanura), rifleman, tomtit, and tui (Prosthemadera novaeseelandiae) with a delayed positive response of the largest species 2.5 years after control (the New Zealand pigeon (Hemiphaga novaeseelandiae). In my final data chapter, I focus on the nesting outcomes of a common endemic species, the North Island fantail (Rhipidura fuliginosa placabilis), to different densities of ship rats. Through intensive monitoring of over 100 fantail nests, I estimated the outcomes of nesting attempts and formulated a DIF where nesting success was modelled as a function of the abundance of ship rats at the nest micro-site. Nesting attempts suffered higher failure rates at sites with higher rat abundance however, in this study I also identified a feature of nest placement that apparently limits predation from mammals. Nests placed on thinner branches were more likely to survive rat predation, a neat trick that perhaps only the smallest of birds can manage. My thesis identifies some species as particularly vulnerable to invasive mammalian predation while others are more resilient. Understanding resilience and vulnerability in New Zealand’s bird species sheds light on historical extinctions and the processes that continue to mould New Zealand's avifauna. I quantified responses of New Zealand forest bird species, to different levels of invasive mammal management and residual densities of mammals, with consideration of climate and forest productivity. These estimates could be applied by conservation managers to more effectively gauge future threats to native avifauna according to the attributes of bird species and present and future management scenarios.</p>

The responses of New Zealand's arboreal forest birds to invasive mammal control

<p>Introduced mammalian predators are responsible for over half of contemporary extinctions and declines of birds. Endemic bird species on islands are particularly vulnerable to invasions of mammalian predators. The native bird species that remain in New Zealand forests continue to be threatened by predation from invasive mammals, with brushtail possums (Trichosurus vulpecula) ship rats (Rattus rattus) and stoats (Mustela erminea) identified as the primary agents responsible for their ongoing decline. Extensive efforts to suppress these pests across New Zealand’s forests have created "management experiments" with potential to provide insights into the ecological forces structuring forest bird communities. To understand the effects of invasive mammals on birds, I studied responses of New Zealand bird species at different temporal and spatial scales to different intensities of control and residual densities of mammals. In my first empirical chapter (Chapter 2), I present two meta-analyses of bird responses to invasive mammal control. I collate data from biodiversity projects across New Zealand where long-term monitoring of arboreal bird species was undertaken. The projects cover a range of treatments including fenced sanctuaries, offshore islands, forests treated periodically and sites lacking significant mammal control. I found that New Zealand bird species exhibit complex responses to the varied and sustained management effort that has occurred across New Zealand’s landscape in the last fifty years. Some species show significant positive outcomes to control, notably the larger endemic species, while others, including highly endemic species, consistently decline after control. In Chapter 3, I estimate the responses of bird populations in the central New Zealand region to changes in ship rat densities. I collaborated with scientists from the Department of Conservation (DOC) and Greater Wellington Regional Council and collated biodiversity data from four restoration projects located across the central New Zealand region. I constructed multiple density impact functions (DIFs), where the effect of a change in density of a pest on a valued resource is quantified, to describe the impacts of ship rat population dynamics on native bird populations. These responses were then modelled in a meta-analysis to provide overall effects for bird populations when rat abundance increases. I identified two taxa that exhibit significant negative responses across the region: the native parakeet species (Cyanoramphus spp.) and the tomtit (Petroica macrocephala). Evidence from single projects also showed that two other species were negatively affected by increases in rats: the South Island kaka (Nestor meridionalis) and the North Island rifleman (Acanthisitta chloris). Conversely, populations of the recently introduced silvereye (Zosterops lateralis) were resilient to rat population recovery as silvereye counts significantly increased the year after an increase in ship rat populations was observed. In Chapter 4, I monitored bird species through a 1080 mammal-control operation in the southern Wairarapa. This operation coincided with a heavy beech mast, an irruptive event that occurs every 2-6 years. Most likely because of the abundance of seed, suppression of ship rats and possums appeared to be short-lived, and detections of these two mammals returned to pre-control levels within one and two years, respectively. Short-term responses of native birds to the control operation were positive: initially, for the small-medium sized bird species (i.e. the bellbird (Anthornis melanura), rifleman, tomtit, and tui (Prosthemadera novaeseelandiae) with a delayed positive response of the largest species 2.5 years after control (the New Zealand pigeon (Hemiphaga novaeseelandiae). In my final data chapter, I focus on the nesting outcomes of a common endemic species, the North Island fantail (Rhipidura fuliginosa placabilis), to different densities of ship rats. Through intensive monitoring of over 100 fantail nests, I estimated the outcomes of nesting attempts and formulated a DIF where nesting success was modelled as a function of the abundance of ship rats at the nest micro-site. Nesting attempts suffered higher failure rates at sites with higher rat abundance however, in this study I also identified a feature of nest placement that apparently limits predation from mammals. Nests placed on thinner branches were more likely to survive rat predation, a neat trick that perhaps only the smallest of birds can manage. My thesis identifies some species as particularly vulnerable to invasive mammalian predation while others are more resilient. Understanding resilience and vulnerability in New Zealand’s bird species sheds light on historical extinctions and the processes that continue to mould New Zealand's avifauna. I quantified responses of New Zealand forest bird species, to different levels of invasive mammal management and residual densities of mammals, with consideration of climate and forest productivity. These estimates could be applied by conservation managers to more effectively gauge future threats to native avifauna according to the attributes of bird species and present and future management scenarios.</p>

Vocal Communication Within a Forest Bird Community

<p><b>This thesis takes a community approach to investigate the acoustics of forest birds in Zealandia sanctuary, Wellington. Initially, the annual changes in vocalisation output of 16 study species and their possible effect on bird conspicuousness were described. Environmental factors that may shape these avian vocalisations were addressed though invoking two key hypotheses, the acoustic adaptation hypothesis, and the acoustic niche hypothesis. In addition, the songs of selected species are investigated: the role of song harmonics in the native North Island saddleback, Philesturnus rufusater, and their role in ranging, change in song dialect through time and space in the introduced song thrush, Turdus philomelos, and temporal change in the song of the native grey warbler, Greygone igata. Vocal activity of the study species varied seasonally, affecting their detectability in bird counts. Some species were mostly first heard rather than seen and viceversa. The results lend support to the acoustic niche hypothesis in that vocalisations within the forest bird community appear to have evolved towards divergence, with native species’ vocalisations being more dispersed within the community acoustic space than those of the introduced species. However, all species concentrated their energy within relatively narrow frequency bands, supporting the predictions of the acoustic adaptation hypothesis. Adaptation to different transmission properties associated with different singing elevations or physiological parameters such as body weight may have an effect on shaping such bird vocalisations.</b></p> <p>Forests provide a complex acoustic space for sound transmission and a “sound window” may not be a constant property of a given forest. The study revealed that a prominent sound window persists in the lower frequency range that is less affected by habitat. Some high frequencies may have similar average attenuation values to those of low frequency, however, with greater fluctuation in attenuation. Ground effect is a further factor in determining how well different frequency ranges transmit and birds may use acoustic characteristics of their habitat to enhance their signal.</p> <p>Harmonics in North Island saddleback chatter song were found to play a potential role in ranging (estimating the distance of signaller), for playback songs with more relative energy within higher harmonics were evidently perceived as coming from a nearby individual.</p> <p>The repertoire size of the song thrush population studied in Zealandia has apparently evolved to become larger and more varied than the source population of song thrushes in the UK, with more syllables delivered with less repetition than the UK song recordings examined.</p> <p>Over a period of 7 years, syllables in grey warbler song have shifted to a higher frequency, but there was no difference in the temporal structure of the song. Habitat effect, competition on the acoustic signal from reintroduced birds and ambient noise level are considered as possible casual factors.</p>

Vocal Communication Within a Forest Bird Community

<p><b>This thesis takes a community approach to investigate the acoustics of forest birds in Zealandia sanctuary, Wellington. Initially, the annual changes in vocalisation output of 16 study species and their possible effect on bird conspicuousness were described. Environmental factors that may shape these avian vocalisations were addressed though invoking two key hypotheses, the acoustic adaptation hypothesis, and the acoustic niche hypothesis. In addition, the songs of selected species are investigated: the role of song harmonics in the native North Island saddleback, Philesturnus rufusater, and their role in ranging, change in song dialect through time and space in the introduced song thrush, Turdus philomelos, and temporal change in the song of the native grey warbler, Greygone igata. Vocal activity of the study species varied seasonally, affecting their detectability in bird counts. Some species were mostly first heard rather than seen and viceversa. The results lend support to the acoustic niche hypothesis in that vocalisations within the forest bird community appear to have evolved towards divergence, with native species’ vocalisations being more dispersed within the community acoustic space than those of the introduced species. However, all species concentrated their energy within relatively narrow frequency bands, supporting the predictions of the acoustic adaptation hypothesis. Adaptation to different transmission properties associated with different singing elevations or physiological parameters such as body weight may have an effect on shaping such bird vocalisations.</b></p> <p>Forests provide a complex acoustic space for sound transmission and a “sound window” may not be a constant property of a given forest. The study revealed that a prominent sound window persists in the lower frequency range that is less affected by habitat. Some high frequencies may have similar average attenuation values to those of low frequency, however, with greater fluctuation in attenuation. Ground effect is a further factor in determining how well different frequency ranges transmit and birds may use acoustic characteristics of their habitat to enhance their signal.</p> <p>Harmonics in North Island saddleback chatter song were found to play a potential role in ranging (estimating the distance of signaller), for playback songs with more relative energy within higher harmonics were evidently perceived as coming from a nearby individual.</p> <p>The repertoire size of the song thrush population studied in Zealandia has apparently evolved to become larger and more varied than the source population of song thrushes in the UK, with more syllables delivered with less repetition than the UK song recordings examined.</p> <p>Over a period of 7 years, syllables in grey warbler song have shifted to a higher frequency, but there was no difference in the temporal structure of the song. Habitat effect, competition on the acoustic signal from reintroduced birds and ambient noise level are considered as possible casual factors.</p>

Timing Is Everything: Acoustic Niche Partitioning in Two Tropical Wet Forest Bird Communities

When acoustic signals sent from individuals overlap in frequency and time, acoustic interference and signal masking may occur. Under the acoustic niche hypothesis (ANH), signaling behavior has evolved to partition acoustic space and minimize overlap with other calling individuals through selection on signal structure and/or the sender’s ability to adjust the timing of signals. Alternately, under the acoustic clustering hypothesis, there is potential benefit to convergence and synchronization of the structural or temporal characteristics of signals in the avian community, and organisms produce signals that overlap more than would be expected by chance. Interactive communication networks may also occur, where species living together are more likely to have songs with convergent spectral and or temporal characteristics. In this study, we examine the fine-scale use of acoustic space in montane tropical wet forest bird communities in Costa Rica and Hawai‘i. At multiple recording stations in each community, we identified the species associated with each recorded signal, measured observed signal overlap, and used null models to generate random distributions of expected signal overlap. We then compared observed vs. expected signal overlap to test predictions of the acoustic niche and acoustic clustering hypotheses. We found a high degree of overlap in the signal characteristics (frequency range) of species in both Costa Rica and Hawai‘i, however, as predicted under ANH, species significantly reduced observed overlap relative to the random distribution through temporal partitioning. There was little support for acoustic clustering or the prediction of the network hypothesis that species segregate across the landscape based on the frequency range of their vocalizations. These findings constitute strong support that there is competition for acoustic space in these signaling communities, and this has resulted primarily in temporal partitioning of the soundscape.