Core and Shell Song Systems Unique to the Parrot Brain.

The ability to imitate complex sounds is rare, and among birds has been found only in parrots, songbirds, and hummingbirds. Parrots exhibit the most advanced vocal mimicry among non-human animals. A few studies have noted differences in connectivity, brain position and shape in the vocal learning systems of parrots relative to songbirds and hummingbirds. However, only one parrot species, the budgerigar, has been examined and no differences in the presence of song system structures were found with other avian vocal learners. Motivated by questions of whether there are important differences in the vocal systems of parrots relative to other vocal learners, we used specialized constitutive gene expression, singing-driven gene expression, and neural connectivity tracing experiments to further characterize the song system of budgerigars and/or other parrots. We found that the parrot brain uniquely contains a song system within a song system. The parrot "core" song system is similar to the song systems of songbirds and hummingbirds, whereas the "shell" song system is unique to parrots. The core with only rudimentary shell regions were found in the New Zealand kea, representing one of the only living species at a basal divergence with all other parrots, implying that parrots evolved vocal learning systems at least 29 million years ago. Relative size differences in the core and shell regions occur among species, which we suggest could be related to species differences in vocal and cognitive abilities.

Comparative analyses of clinical and environmental populations of Cryptococcus neoformans in Botswana.

Cryptococcus neoformans var. grubii (Cng) is the most common cause of fungal meningitis, and its prevalence is highest in sub-Saharan Africa. Patients become infected by inhaling airborne spores or desiccated yeast cells from the environment, where the fungus thrives in avian droppings, trees and soil. To investigate the prevalence and population structure of Cng in southern Africa, we analysed isolates from 77 environmental samples and 64 patients. We detected significant genetic diversity among isolates and strong evidence of geographic structure at the local level. High proportions of isolates with the rare MATa allele were observed in both clinical and environmental isolates; however, the mating-type alleles were unevenly distributed among different subpopulations. Nearly equal proportions of the MATa and MATα mating types were observed among all clinical isolates and in one environmental subpopulation from the eastern part of Botswana. As previously reported, there was evidence of both clonality and recombination in different geographic areas. These results provide a foundation for subsequent genomewide association studies to identify genes and genotypes linked to pathogenicity in humans.

Gene loss, adaptive evolution and the co-evolution of plumage coloration genes with opsins in birds.

BACKGROUND: The wide range of complex photic systems observed in birds exemplifies one of their key evolutionary adaptions, a well-developed visual system. However, genomic approaches have yet to be used to disentangle the evolutionary mechanisms that govern evolution of avian visual systems. RESULTS: We performed comparative genomic analyses across 48 avian genomes that span extant bird phylogenetic diversity to assess evolutionary changes in the 17 representatives of the opsin gene family and five plumage coloration genes. Our analyses suggest modern birds have maintained a repertoire of up to 15 opsins. Synteny analyses indicate that PARA and PARIE pineal opsins were lost, probably in conjunction with the degeneration of the parietal organ. Eleven of the 15 avian opsins evolved in a non-neutral pattern, confirming the adaptive importance of vision in birds. Visual conopsins sw1, sw2 and lw evolved under negative selection, while the dim-light RH1 photopigment diversified. The evolutionary patterns of sw1 and of violet/ultraviolet sensitivity in birds suggest that avian ancestors had violet-sensitive vision. Additionally, we demonstrate an adaptive association between the RH2 opsin and the MC1R plumage color gene, suggesting that plumage coloration has been photic mediated. At the intra-avian level we observed some unique adaptive patterns. For example, barn owl showed early signs of pseudogenization in RH2, perhaps in response to nocturnal behavior, and penguins had amino acid deletions in RH2 sites responsible for the red shift and retinal binding. These patterns in the barn owl and penguins were convergent with adaptive strategies in nocturnal and aquatic mammals, respectively. CONCLUSIONS: We conclude that birds have evolved diverse opsin adaptations through gene loss, adaptive selection and coevolution with plumage coloration, and that differentiated selective patterns at the species level suggest novel photic pressures to influence evolutionary patterns of more-recent lineages.

The Origin and Diversification of Birds.

Birds are one of the most recognizable and diverse groups of modern vertebrates. Over the past two decades, a wealth of new fossil discoveries and phylogenetic and macroevolutionary studies has transformed our understanding of how birds originated and became so successful. Birds evolved from theropod dinosaurs during the Jurassic (around 165-150 million years ago) and their classic small, lightweight, feathered, and winged body plan was pieced together gradually over tens of millions of years of evolution rather than in one burst of innovation. Early birds diversified throughout the Jurassic and Cretaceous, becoming capable fliers with supercharged growth rates, but were decimated at the end-Cretaceous extinction alongside their close dinosaurian relatives. After the mass extinction, modern birds (members of the avian crown group) explosively diversified, culminating in more than 10,000 species distributed worldwide today.

Response to Comment on "Whole-genome analyses resolve early branches in the tree of life of modern birds".

Mitchell et al. argue that divergence-time estimates for our avian phylogeny were too young because of an "inappropriate" maximum age constraint for the most recent common ancestor of modern birds and that, as a result, most modern bird orders diverged before the Cretaceous-Paleogene mass extinction event 66 million years ago instead of after. However, their interpretations of the fossil record and timetrees are incorrect.

RED COATS AND WILD BIRDS: MILITARY CULTURE AND ORNITHOLOGY ACROSS THE NINETEENTH-CENTURY BRITISH EMPIRE

“Red coats and wild birds: military culture and ornithology across the nineteenth-century British Empire” investigates the intersections between British military culture and the practices and ideas of ornithology, with a particular focus on the British Mediterranean. Considering that British officers often occupied several imperial sites over the course of their military careers, to what extent did their movements shape their ornithological knowledge and identities at “home” and abroad? How did British military naturalists perceive different local cultures (with different attitudes to hunting, birds, field science, etc.) and different local natures (different sets of birds and environments)? How can trans-imperial careers be written using not only textual sources (for example, biographies and personal correspondence) but also traces of material culture? In answering these questions, I centre my work on the Mediterranean region as a “colonial sea” in the production of hybrid identities and cultural practices, and the mingling of people, ideas, commodities, and migratory birds. I focus on the life geographies of four military officers: Thomas Wright Blakiston, Andrew Leith Adams, L. Howard Lloyd Irby, and Philip Savile Grey Reid. By the mid-nineteenth century, the Mediterranean region emerged as a crucial site for the security of the British “empire route” to India and South Asia, especially with the opening of the Suez Canal in 1869. Military stations served as trans-imperial sites, connecting Britain to India through the flow of military manpower, commodities, information, and bodily experiences across the empire. By using a “critical historical geopolitics of empire” to examine the material remnants of the “avian imperial archive,” I demonstrate how the practices and performances of British military field ornithology helped to: materialize the British Mediterranean as a moral “semi-tropical” place for the physical and cultural acclimatization of British officers en route to and from India; reinforce imperial presence in the region; and make “visible in new ways” the connectivity of North Africa to Europe through the geographical distribution of birds. I also highlight the ways in which the production of ornithological knowledge by army officers was entwined with forms of temperate martial masculinity.

Conservation of substrate specificities among coronavirus main proteases.

The key enzyme in coronavirus replicase polyprotein processing is the coronavirus main protease, 3CL(pro). The substrate specificities of five coronavirus main proteases, including the prototypic enzymes from the coronavirus groups I, II and III, were characterized. Recombinant main proteases of human coronavirus (HCoV), transmissible gastroenteritis virus (TGEV), feline infectious peritonitis virus, avian infectious bronchitis virus and mouse hepatitis virus (MHV) were tested in peptide-based trans-cleavage assays. The determination of relative rate constants for a set of corresponding HCoV, TGEV and MHV 3CL(pro) cleavage sites revealed a conserved ranking of these sites. Furthermore, a synthetic peptide representing the N-terminal HCoV 3CL(pro) cleavage site was shown to be effectively hydrolysed by noncognate main proteases. The data show that the differential cleavage kinetics of sites within pp1a/pp1ab are a conserved feature of coronavirus main proteases and lead us to predict similar processing kinetics for the replicase polyproteins of all coronaviruses.

The natural plasma testosterone profile of male blue tits during the breeding season and its relation to song output

In male birds, the gonadal hormone testosterone (T) is known to influence territorial and mating behaviour. Plasma levels of T show seasonal fluctuations which vary in relation to mating system and social instability. First, we determined the natural T profile of male blue tits Parus caeruleus during the breeding season. We found that plasma levels of T increased at the onset of nest building. Thus, the increase in circulating T was not associated with territory establishment, nor with the fertile period of the males' mates. In most individuals, T levels dropped to values close to zero during the period of chick feeding. Second, we investigated the relationship between plasma levels of T and male age, size, and singing behaviour. During the mating period, T levels did not differ between 1 yr old and older males and did not correlate with body size or condition. However, song output during the dawn chorus tended to be positively correlated with T levels. Therefore, if high T levels are costly, song output might be an honest indicator of male quality in blue tits. Finally, we show that plasma levels of T are significantly higher during the night than during the day. This pattern has also been observed in captive non-passerine birds, but its functional significance remains unknown.

Future novel threats and opportunities facing UK biodiversity identified by horizon scanning

1. Horizon scanning is an essential tool for environmental scientists if they are to contribute to the evidence base for Government, its agencies and other decision makers to devise and implement environmental policies. The implication of not foreseeing issues that are foreseeable is illustrated by the contentious responses to genetically modified herbicide-tolerant crops in the UK, and by challenges surrounding biofuels, foot and mouth disease, avian influenza and climate change.

Further evidence for visual landmark involvement in the pigeon's familiar area map

In previous experiments suggesting that previewing visual landscapes speeds homing from familiar release sites, restricted access to olfactory cues may have artefactually encouraged homing pigeons, Calumba livia, to resort to visual landmark orientation. Since evidence for the role of visual landmarks in wide-ranging avian orientation is still equivocal, Braithwaite & Guilford's (1991, Proc. R. Sec. Lond. Ser. B, 245, 183-186) 'previewing' experiments were replicated: birds were allowed or denied visual access to a familiar site prior to release, but allowed ample access to olfactory cues. In experiment 1, allowing birds to preview familiar sites for 5 min prior to release enhanced homing speeds by about 12%. In experiment 2, modified to reduce between-day effects on variation, previewing enhanced homing speeds by about 16%. These experiments support the conclusion that visual landmarks remote from sight of the loft are an important component of the familiar area map, although the nature of the landmarks and how they are encoded remain to be determined. (C) 1997 The Association for the Study of Animal Behaviour.

‘Invasional meltdown’: evidence for unexpected consequences and cumulative impacts of multispecies invasions

Empirical support for ‘invasional meltdown’, where the presence of one invading species facilitates another and compounds negative impacts on indigenous species, is equivocal with few convincing studies. In Ireland, the bank vole was introduced 80 years ago and now occupies a third of the island. The greater white-toothed shrew arrived more recently within the invasive range of the bank vole. We surveyed the abundance of both invasive species and two indigenous species, the wood mouse and pygmy shrew, throughout their respective ranges. The negative effects of invasive on indigenous species were strong and cumulative bringing about species replacement. The greater white-toothed shrew, the second invader, had a positive and synergistic effect on the abundance of the bank vole, the first invader, but a negative and compounding effect on the abundance of the wood mouse and occurrence of the pygmy shrew. The gradual replacement of the wood mouse by the bank vole decreased with distance from the point of the bank vole’s introduction whilst no pygmy shrews were captured where both invasive species were present. Such interactions may not be unique to invasions but characteristic of all multispecies communities. Small mammals are central in terrestrial food webs and compositional changes to this community in Ireland are likely to reverberate throughout the ecosystem. Vegetation composition and structure, invertebrate communities and the productivity of avian and mammalian predators are likely to be affected. Control of these invasive species may only be effected through landscape and habitat management.

Immunological variants of the aerobactin-cloacin DF13 outer membrane protein receptor IutA among enteric bacteria

Mouse monoclonal antibodies (MAbs) were generated against a 76-kDa IutA receptor of pathogenic avian Escherichia coli 15972. Six of the eight IutA-specific MAbs isolated (AB1 to AB6) were shown to be directed toward membrane-exposed conformational epitopes, although they did not interfere with the uptake of ferric aerobactin and cloacin DF13 as assessed by competition experiments with purified ligands. The two remaining IutA MAbs (AB9 and AB10) recognized linear epitopes buried in the IutA molecule. The panel of IutA MAbs was used to characterize IutA variants occurring in strains of E. coli, Klebsiella pneumoniae, Enterobacter spp., and Shigella spp., resulting in the identification of four immunological groups of IutAs. MAb AB9 defined an epitope conserved in all IutA variants. In addition, the panel of IutA MAbs served to identify the presence of IutA in wild-type bacteria grown in the presence of diphenylamine to reduce the expression of O-specific polysaccharide.

Morbillivirus cross-species infection:is there a risk for humans?

The World Health Organisation (WHO) has set regional elimination goals for Measles (MV) eradication to be achieved by 2020 or earlier. A major question is whether an opportunity for veterinary virus infection of humans may arise when MV is eradicated and if vaccination is discontinued. Lessons have been learned from animal to human virus transmission i.e. human immunodeficiency virus (HIV) and more recently from severe acute respiratory syndrome (SARS) and avian influenza virus infections. We are therefore alerted to the risk of zoonosis from the veterinary morbilliviruses. In this review the evidence from viral genomics, animal studies and cell culture experiments will be explored to evaluate the possibility of cross infection of humans with these viruses.

Analysis of nine NSAIDs in ungulate tissues available to critically endangered vultures in India

In 2006, India, Pakistan, and Nepal banned the manufacture of veterinary formulations of the nonsteroidal anti-inflammatory drug (NSAID) diclofenac. This action was taken to halt the unprecedented decline of three Gyps vulture species that were being poisoned by diclofenac residues commonly present in carcasses of domestic livestock upon which they scavenged. To assess the affect of this ban and evaluate residue prevelances of other NSAIDs, we present a method to detect diclofenac and eight more NSAIDs by liquid chromatography-mass spectrometry and apply this to 1488 liver samples from carcasses of livestock taken across seven Indian states. Diclofenac was present in 11.1% of samples taken between April and December 2006, and meloxicam (4%), ibuprofen (0.6%), and ketoprofen (0.5%) were also detected. Although meloxicam is safe for a range of avian scavengers, including Gypsvultures, data regarding the safety of other NSAIDs is currently limited. If wild Gyps on the Indian subcontinent are to survive, diclofenac bans must be completely effective, and NSAIDs that replace it within the veterinary drug market must be of low toxicity toward Gyps and other scavenging birds.