The effects of sympatry on patterns of bill morphology between closely related species of birds, worldwide

When closely related species co-occur in sympatry, they face a significant challenge. They must adapt to the same local conditions in their shared environment, which favours the convergent evolution of traits, while simultaneously minimizing the costs of competition for shared resources that typically favours the divergent evolution of traits. Here, we use a comparative sister lineage approach to test how most species have responded to these conflicting selection pressures in sympatry, focusing on a key ecological trait: the bill morphology of birds. If similar bill morphologies incur fitness costs due to species interactions, then we predicted that the bill morphologies of closely related species would differ more in sympatry compared with allopatry. Alternatively, if similar bill morphologies incur fitness benefits due to local adaptation, then we predicted that the bill morphologies would be more similar in sympatry compared with allopatry. We used museum specimens to measure five aspects of bill (maxilla) morphology – depth, length, width, side shape, and bottom shape – in diverse bird species from around the world to test our alternative hypotheses. We found support for both divergent evolution and convergent evolution (or trait retention) in one ecological trait: closely related sympatric species diverged in bill depth, but converged in side shape. These patterns of bill evolution were influenced by the genetic distance between closely related sister taxa and the geographic distance between allopatric lineages. Overall, our results highlight species interactions as an important mechanism for the evolution of some (bill depth), but not all (bill shape), aspects of bill morphology in closely related species in sympatry, and provide strong support for the bill as a key ecological trait that can adapt in different ways to the conflicting challenges of sympatry.

A metagenomic comparison of endemic viruses from broiler chickens with runting stunting syndrome and from normal birds

Runting-stunting syndrome (RSS) in broiler chickens is an enteric disease that causes significant economic losses to poultry producers worldwide due to elevated feed conversion ratios, decreased body weight during growth, and excessive culling. Of specific interest are the viral agents associated with RSS which have been difficult to fully characterise to date. Past research into the aetiology of RSS has implicated a wide variety of RNA and DNA viruses however, to date, no individual virus has been identified as the main agent of RSS and the current opinion is that it may be caused by a community of viruses, collectively known as the virome. This paper attempts to characterise the viral pathogens associated with 2 – 3 week old RSS-affected and unaffected broiler chickens using next-generation sequencing and comparative metagenomics. Analysis of the viromes identified a total of 20 DNA & RNA viral families, along with 2 unidentified categories, comprised of 31 distinct viral genera and 7 unclassified genera. The most abundant viral families identified in this study were the Astroviridae, Caliciviridae, Picornaviridae, Parvoviridae, Coronaviridae, Siphoviridae, and Myoviridae. This study has identified historically significant viruses associated with the disease such as chicken astrovirus, avian nephritis virus, chicken parvovirus, and chicken calicivirus along with relatively novel viruses such as chicken megrivirus and sicinivirus 1 and will help expand the knowledge related to enteric disease in broiler chickens, provide insights into the viral constituents of a healthy avian gut, and identify a variety of enteric viruses and viral communities appropriate for further study.

Early post-fledgling survival in a fragmented population of a tropical cooperative breeding passerine

During the last years tropical forest has been a target of intense study especially due to its recent big scale destruction. Although a lot still needs to be explored, we start realizing how negative can the impact of our actions be for the ecosystem. Subsequently, the living community have been developing strategies to overcome this problem avoiding bottlenecks or even extinctions. Cooperative breeding (CB) has been recently pointed out as one of those strategies. CB is a breeding system where more than two individuals raise one brood. In most of the cases, extra individuals are offspring that delay their dispersal and independent breeding what allows them to help their parents raising their siblings in the subsequent breeding season. Such behavior is believed to be due, per example, to the lack of mates or breeding territories (ecological constraints hypothesis), a consequence of habitat fragmentation and/or disturbance. From this point, CB is easily promoted by a higher reproductive success of group vs pairs or single individuals. Accordingly, during this thesis I explore the early post-fledging survival of a cooperative breeding passerine, namely the impact of individual/habitat quality in its survival probability during the dependence period of the chicks. Our study species is the Cabanis’s greenbul (Phyllastrephus cabanisi), a medium-sized, brownish passerine, classified within the Pycnonotidae family. It is found over part of Central Africa in countries such as Angola, Democratic Republic of the Congo, Mozambique and Kenya, inhabiting primary and secondary forests, as well as woodland of various types up to 2700m of altitude. Previous studies have concluded that PC is a facultative cooperative breeder. This study was conducted in Taita Hills (TH) at the Eastern Arc Mountains (EAM), a chain of mountains running from Southeast Kenya to the South of Tanzania. TH comprises an area of 430 ha and has been suffering intense deforestation reflecting 98% forest reduction over the last 200 years. Nowadays its forest is divided in fragments and our study was based in 5of those fragments. We access the post-fledging survival through radio-telemetry. The juvenile survey was done through the breeding females in which transmitters were placed with a leg-loop technique. Ptilochronology is consider to be the study of feather growth bars and has been used to study the nutritional state of a bird. This technique considers that the feather growth rate is positively proportional to the individual capability of ingesting food and to the food availability. This technique is therefore used to infer for individual/habitat quality. Survival was lowest during the first 5 days post-fledging representing 53.3%. During the next 15 days, risk of predation decreased with only 14.3% more deceased individuals. This represents a total of only 33% survived individuals in the end of the 50 days. Our results showed yet a significant positive relationship between flock size and post-fledging survival as well as between ptilochronology values and post-fledgling survival. In practice, these imply that on this population, as bigger the flock, as greater the post fledging survival and that good habitat quality or good BF quality, will lead to a higher juvenile survival rate. We believe that CB is therefore an adaptive behaviour to the lack of mates/breeding territory originated from the mass forest destruction and disturbance. Such results confirms the critical importance of habitat quality in the post-fledging survival and, for the first time, demonstrates how flock size influences the living probability of the juveniles and therefore how it impacts the (local) population dynamics of this species. In my opinion, future research should be focus in disentangle individual and habitat quality from each other and verify which relationship exist between them. Such study will allow us to understand which factor has a stronger influence in the post-fledging survival and therefore redirect our studies in that direction. In order to confirm the negative impact of human disturbance and forest fragmentation, it would be of major relevance to compare the reproductive strategies and reproductive success of populations living in intact forests and disturbed patches.

Ecological drivers of a vector borne pathogen: distribution and abundance of Borrelia burgdorferi sensu lato and its vector Ixodes ricinus in Scotland

Vector-borne disease emergence in recent decades has been associated with different environmental drivers including changes in habitat, hosts and climate. Lyme borreliosis is among the most important vector-borne diseases in the Northern hemisphere and is an emerging disease in Scotland. Transmitted by Ixodid tick vectors between large numbers of wild vertebrate host species, Lyme borreliosis is caused by bacteria from the Borrelia burgdorferi sensu lato species group. Ecological studies can inform how environmental factors such as host abundance and community composition, habitat and landscape heterogeneity contribute to spatial and temporal variation in risk from B. burgdorferi s.l. In this thesis a range of approaches were used to investigate the effects of vertebrate host communities and individual host species as drivers of B. burgdorferi s.l. dynamics and its tick vector Ixodes ricinus. Host species differ in reservoir competence for B. burgdorferi s.l. and as hosts for ticks. Deer are incompetent transmission hosts for B. burgdorferi s.l. but are significant hosts of all life-stages of I. ricinus. Rodents and birds are important transmission hosts of B. burgdorferi s.l. and common hosts of immature life-stages of I. ricinus. In this thesis, surveys of woodland sites revealed variable effects of deer density on B. burgdorferi prevalence, from no effect (Chapter 2) to a possible ‘dilution’ effect resulting in lower prevalence at higher deer densities (Chapter 3). An invasive species in Scotland, the grey squirrel (Sciurus carolinensis), was found to host diverse genotypes of B. burgdorferi s.l. and may act as a spill-over host for strains maintained by native host species (Chapter 4). Habitat fragmentation may alter the dynamics of B. burgdorferi s.l. via effects on the host community and host movements. In this thesis, there was lack of persistence of the rodent associated genospecies of B. burgdorferi s.l. within a naturally fragmented landscape (Chapter 3). Rodent host biology, particularly population cycles and dispersal ability are likely to affect pathogen persistence and recolonization in fragmented habitats. Heterogeneity in disease dynamics can occur spatially and temporally due to differences in the host community, habitat and climatic factors. Higher numbers of I. ricinus nymphs, and a higher probability of detecting a nymph infected with B. burgdorferi s.l., were found in areas with warmer climates estimated by growing degree days (Chapter 2). The ground vegetation type associated with the highest number of I. ricinus nymphs varied between studies in this thesis (Chapter 2 & 3) and does not appear to be a reliable predictor across large areas. B. burgdorferi s.l. prevalence and genospecies composition was highly variable for the same sites sampled in subsequent years (Chapter 2). This suggests that dynamic variables such as reservoir host densities and deer should be measured as well as more static habitat and climatic factors to understand the drivers of B. burgdorferi s.l. infection in ticks. Heterogeneity in parasite loads amongst hosts is a common finding which has implications for disease ecology and management. Using a 17-year data set for tick infestations in a wild bird community in Scotland, different effects of age and sex on tick burdens were found among four species of passerine bird (Chapter 5). There were also different rates of decline in tick burdens among bird species in response to a long term decrease in questing tick pressure over the study. Species specific patterns may be driven by differences in behaviour and immunity and highlight the importance of comparative approaches. Combining whole genome sequencing (WGS) and population genetics approaches offers a novel approach to identify ecological drivers of pathogen populations. An initial analysis of WGS from B. burgdorferi s.s. isolates sampled 16 years apart suggests that there is a signal of measurable evolution (Chapter 6). This suggests demographic analyses may be applied to understand ecological and evolutionary processes of these bacteria. This work shows how host communities, habitat and climatic factors can affect the local transmission dynamics of B. burgdorferi s.l. and the potential risk of infection to humans. Spatial and temporal heterogeneity in pathogen dynamics poses challenges for the prediction of risk. New tools such as WGS of the pathogen (Chapter 6) and blood meal analysis techniques will add power to future studies on the ecology and evolution of B. burgdorferi s.l.

A natural history of the globe, of man, of beasts, birds, fishes, reptiles, insects and plants.

"The English edition of this work appeared under the title of 'Buffon's Natural history, &c.'"

Birds of a feather: the geographic interconnection of Australian universities on Twitter

Purpose
Regardless of their virtual nature, research suggests that social media networks are still influenced by geography. This research investigates the connections between Australian universities on the Twitter social media system.

Design/methodology/approach
This research employs network analysis and visualisation to characterise the connections between Australian universities on Twitter.

Findings
A strong relationship to geography, both at the intra-state level and the inter-state level, was observed in the connections between Australian universities on Twitter. A relationship between number of followers and time since joining Twitter was also observed.

Research limitations/implications
The research presented is limited to Australian universities only and represents a snapshot in time only.

Practical implications
Australian universities have the opportunity to reach beyond the geographically restricted connections observed here, to actively seek new audiences, and to realise the cited benefits of online social media relating to increased connection across physical and digital frontiers. By capitalising on the strong ‘locality’ observed in social media connections, a university could become a desirable source of information that is likely to be of interest to, and valued by, local constituents.

Originality/value
This paper contributes to the research literature on university use of social media by addressing the so far largely silent area of inter-institutional connections via social media, and the influence of physical geography on the connections between universities on Twitter. It also offers a practical methodology for those interested in further research in this area.

Complex responses of birds to landscape-level fire extent, fire severity and environmental drivers

Aim: To quantify bird responses to a large unplanned fire, taking into consideration landscape-level fire severity and extent, pre-fire site detection frequency and environmental gradients. Location: South-eastern Australia. Methods: A major wildfire in 2009 coincided with a long-term study of birds and provided a rare opportunity to quantify bird responses to wildfire. Using hierarchical Bayesian analysis, we modelled bird species richness and the detection frequency of individual species in response to a suite of explanatory variables, including (1) landscape-level fire severity and extent (2) pre-fire detection frequency, (3) site-level vegetation density and (4) environmental variables (e.g. elevation and topography). Results: Landscape-level fire severity had strong effects on bird species richness and the detection frequency of the majority of bird species. These effects varied markedly between species; most responded negatively to amount of severely burned forest in the landscape, one negatively to the amount of moderately burned forest and one responded negatively to the total area of burned forest. Only one species - the Flame Robin - responded positively to the amount of burned forest. Relationships with landscape-scale fire extent changed over time for one species - the Brown Thornbill - with initially depressed rates of detection recovering after just 2 years. The majority of species were significantly more likely to be detected in burned areas if they have been recorded there prior to the fire. Main conclusions: Birds responded strongly to the severity and spatial extent of fire. They also exhibited strong site fidelity even after severe wildfire which causes profound changes in vegetation cover - a response likely influenced by environmental features such as elevation and topography.

Regional drivers of clutch loss reveal important trade-offs for beach-nesting birds

Coastal birds are critical ecosystem constituents on sandy shores, yet are threatened by depressed reproductive success resulting from direct and indirect anthropogenic and natural pressures. Few studies examine clutch fate across the wide range of environments experienced by birds; instead, most focus at the small site scale. We examine survival of model shorebird clutches as an index of true clutch survival at a regional scale (∼200 km), encompassing a variety of geomorphologies, predator communities, and human use regimes in southeast Queensland, Australia. Of the 132 model nests deployed and monitored with cameras, 45 (34%) survived the experimental exposure period. Thirty-five (27%) were lost to flooding, 32 (24%) were depredated, nine (7%) buried by sand, seven (5%) destroyed by people, three (2%) failed by unknown causes, and one (1%) was destroyed by a dog. Clutch fate differed substantially among regions, particularly with respect to losses from flooding and predation. ‘Topographic’ exposure was the main driver of mortality of nests placed close to the drift line near the base of dunes, which were lost to waves (particularly during storms) and to a lesser extent depredation. Predators determined the fate of clutches not lost to waves, with the depredation probability largely influenced by region. Depredation probability declined as nests were backed by higher dunes and were placed closer to vegetation. This study emphasizes the scale at which clutch fate and survival varies within a regional context, the prominence of corvids as egg predators, the significant role of flooding as a source of nest loss, and the multiple trade-offs faced by beach-nesting birds and those that manage them.

Time since urbanization but not encephalisation is associated with increased tolerance of human proximity in birds

The examination of links between a high degree of encephalisation (i.e., a large brain mass relative to body size) and the capacity of wildlife to inhabit anthropogenic habitats has formed the basis of several recent studies, although typically they have not uncovered any relationship. It, however, remains unclear whether encephalisation is directly related to a species' capacity to develop tolerance to human proximity (i.e., a reduction in response to approaching humans). It is also unknown whether such a relationship is related to the size of specific areas of the brain. Using published data on flight-initiation distance (FID), the distance at which animals flee from an approaching human, we estimate the degree of tolerance of human proximity for 42 bird species by comparing FIDs in urban and rural areas, with relatively high and low exposure to humans, respectively. We used a phylogenetic, comparative approach to analyse the relationship of degree of tolerance, and of FID in urban and rural populations more directly, to relative sizes of whole brains (42 species) and brain components (25 species) for the species, and examine the effect of the year that the bird species was first recorded in an urban area (year of urbanization). We demonstrate an interaction between bird habitat and year of urbanization on FIDs. Urban populations of species that have a longer history of inhabiting urban areas have lower FIDs (i.e., birds that were urbanized earlier are more tolerant), which may suggest local selection for birds with reduced responsiveness to humans in urban areas. The pattern is not seen in rural populations of the same species, providing additional evidence that it is greater exposure to humans that has resulted in this tolerance. While we found that forebrain mass and optic lobe mass are influential positive predictors of FID there was no indication that degree of tolerance itself was related to any brain size metric and hence no support for the idea that urban populations of species with larger brains are better able to habituate to human presence. This suggests that processes other than encephalisation explain the high degree of tolerance evident in urban-dwelling birds.

Natural Bagaza virus infection in game birds in southern Spain

In late summer 2010 a mosquito born flavivirus not previously reported in Europe called Bagaza virus (BAGV) caused high mortality in red-legged partridges (Alectoris rufa) and ring-necked pheasants (Phasianus colchicus). We studied clinical findings, lesions and viral antigen distribution in naturally BAGV infected game birds in order to understand the apparently higher impact on red-legged partridges. The disease induced neurologic signs in the two galliform species and, to a lesser extent, in common wood pigeons (Columba palumbus). In red-legged partridges infection by BAGV caused severe haemosiderosis in the liver and spleen that was absent in pheasants and less evident in common wood pigeons. Also, BAGV antigen was present in vascular endothelium in multiple organs in red-legged partridges, and in the spleen in common wood pigeons, while in ring-necked pheasants it was only detected in neurons and glial cells in the brain. These findings indicate tropism of BAGV for endothelial cells and a severe haemolytic process in red-legged partridges in addition to the central nervous lesions that were found in all three species.

Placement of re-nests following predation: are birds managing risk?

Nest predation is the most important source of reproductive failure for many bird species, thus placing nests in 'safe' locations that minimise predation risk is paramount to maximising fitness. After a nest predation event, some species have been shown to manage the risk of nest predation for subsequent re-nesting attempts by moving to a new location, placing re-nests in areas with increased cover, or changing the height above ground at which the re-nest is placed. The extent to which this is an adaptive behaviour for birds in general is not yet clear, as existing studies are almost exclusively restricted to northern hemisphere species and species that do not breed cooperatively. Here, we examined the re-nesting behaviour of Bell Miners (Manorina melanophrys), a species of honeyeater endemic to Australia that is both multi-brooded and also frequently re-nests soon after nesting failure; females can build up to five nests in a breeding season. We tested if these females managed within-season nest predation risk by changing nest site characteristics (height from ground and distance between nests) between successive nesting attempts. We found that female miners did indeed manage predation risk by reducing the height from the ground at which they placed re-nests following predation events, but contrary to our second prediction we found no difference in distances moved to re-nest after females experienced nest predation or successfully rearing young.