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Threats to biodiversity resulting from habitat destruction and deterioration have been documented for many species, whilst climate change is regarded as increasingly impacting upon species' distribution and abundance. However, few studies have disentangled the relative importance of these two drivers in causing recent population declines. We quantify the relative importance of both processes by modelling annual variation in population growth of 18 farmland bird species in the UK as a function of measures of land-use intensity and weather. Modelled together, both had similar explanatory power in accounting for annual fluctuations in population growth. When these models were used to retrodict population trends for each species as a function of annual variation in land-use intensity and weather combined, and separately, retrodictions incorporating land-use intensity were more closely linked to observed population trends than retrodictions based only on weather, and closely matched the UK farmland bird index from 1970 onwards. Despite more stable land-use intensity in recent years, climate change (inferred from weather trends) has not overtaken land-use intensity as the dominant driver of bird populations.

Currently, there is a consensus that biological invasions are one of the most important factors in global change due to their ability to modify structures and functions of many communities. The aim of this work was to provide an exhaustive assessment of the alien birds of Argentina, their routes of entry, impacts, and a synthesis of their attributes. We reviewed and compiled data from a variety of sources and databases on alien birds in Argentina and provide a summary for ten species that had been introduced. Introductions occurred in two peaks, one at the end of the nineteenth century and the other during the 1990s. Most of species entered through the Pampas, Espinal, Bosque and Estepas Patagónica ecoregions between 34° and 50° south. Reasons for these introductions include game birds (Silver Pheasant Lophura nycthemera, California Quail Callipepla californica), domestic consumption (Mallard Anas platyrhynchos, Graylag Goose Anser anser, Rock pigeon Columba livia), pets (European Greenfinch Chloris chloris, European Goldfinch Carduelis carduelis, European Starling Sturnus vulgaris, Crested Myna Acridotheres cristatellus, House Sparrow Passer domesticus). These species occupy ecoregions similar to those of their origins, however most have experienced an expansion in the range of ecological conditions within their new habitats. These species provide opportunity for understanding the dynamics of invasions since they provide a diversity in their ecology and environmental needs.

Since antiquity, the keeping of finches as pets has been common throughout the Mediterranean countries and it remains a widespread hobby to the present day. Since most finches are sourced from the wild this hobby can have implications for their conservation, especially for already imperilled species. We conducted a survey of 257 households in the city of Guelma, in the north-east of Algeria, and of 70 participants to a European Goldfinch Carduelis carduelis show contest in Algiers, to understand the owners’ motives for keeping cage birds and find solutions to mitigate any negative effects on the trade. Keeping and showing finches in Algeria is a male-dominated hobby, especially for the 30–40 year age bracket. Our surveys indicate that almost 60% of households had a cage bird, with the European Goldfinch being the most popular species. With a mean of 0.75 goldfinches per household we estimate that in Guelma alone some 17,000 are kept in captivity. Between 70% and 90% of the owners indicated that their birds were indeed wild-sourced, and over 85% of them were aware of the protected status of the European Goldfinch in Algeria. Our findings underline the need for strict enforcement of existing laws and better targeted awareness campaigns to influence the behaviour of owners in order to reduce the demand for wild specimens.

Bacterial diseases are widespread in pet birds, posing a severe threat in nestlings and birds with weakened immune systems, often resulting in high mortality during the first days after hatching. This study aimed to describe the pathological findings of a natural bacterial co-infection with Klebsiella pneumoniae and Pseudomonas aeruginosa in nestling European goldfinches (Carduelis carduelis), as a cause of mortality after hatching. Eight nestlings kept in a breeding facility showed an inability to move, anorexia, and respiratory distress, and were found dead between 1 and 4 days of life. Gross pathological findings included diffuse pneumonia with edema and multifocal hemorrhages and occasionally hepatic necrosis. On histopathology, the main findings in all examined birds included severe, subacute bronchopneumonia and severe necrotizing hepatitis. Gram-negative bacilli were observed in parabronchial walls, within pulmonary arteries and surrounding hepatocellular necrotic foci. Lungs, livers and kidneys were sampled for bacteriological examination, resulting in two Gram-negative bacterial isolates. Four housekeeping genes (i.e., 16S rRNA; rpoB; khe; ecfX) were amplified and sequenced for bacterial identification at species level. Although K. pneumoniae and P. aeruginosa are common Gram-negative pathogens and are often co-isolated in human bacterial pneumonia, co-infection with these bacteria has not been documented in nestling goldfinches to date. Pathogen identification is essential for formulating a correct etiological diagnosis and further selecting the most appropriate therapeutic strategy.

Avian trichomonosis is a common and widespread disease, traditionally affecting columbids and raptors, and recently emerging among finch populations mainly in Europe. Across Europe, finch trichomonosis is caused by a single clonal strain of Trichomonas gallinae and negatively impacts finch populations. Here, we report an outbreak of finch trichomonosis in the wintering populations of Chloris chloris (European greenfinch) and Carduelis carduelis (European goldfinch) from the Boulonnais, in northern France. The outbreak was detected and monitored by bird ringers during their wintering bird ringing protocols. A total of 105 records from 12 sites were collected during the first quarter of 2017, with 46 and 59 concerning dead and diseased birds, respectively. Fourteen carcasses from two locations were necropsied and screened for multiple pathogens; the only causative agent identified was T. gallinae. Genetic characterization was performed by four markers (small subunit ribosomal RNA, hydrogenosomal iron-hydrogenase, and RNA polymerase II subunit 1 genes, and the internal transcribed spacers (ITS) region) and confirmed the T. gallinae strain to be A1, which affects the finch populations of Europe. This was also confirmed by an ITS-based phylogenetic analysis which further illustrated the diversity of the Trichomonas infecting birds. Preliminary data on the survival and dispersion of infected birds were obtained from ring-returns of diseased individuals. The anthropogenic spread of diseases through bird feeding practices is highlighted and some suggestions to prevent pathogen transmission via backyard supplementary feeders for garden birds are given.

Emerging infectious diseases are increasingly cited as threats to wildlife, livestock and humans alike. They can threaten geographically isolated or critically endangered wildlife populations; however, relatively few studies have clearly demonstrated the extent to which emerging diseases can impact populations of common wildlife species. Here, we report the impact of an emerging protozoal disease on British populations of greenfinch Carduelis chloris and chaffinch Fringilla coelebs, two of the most common birds in Britain. Morphological and molecular analyses showed this to be due to Trichomonas gallinae. Trichomonosis emerged as a novel fatal disease of finches in Britain in 2005 and rapidly became epidemic within greenfinch, and to a lesser extent chaffinch, populations in 2006. By 2007, breeding populations of greenfinches and chaffinches in the geographic region of highest disease incidence had decreased by 35% and 21% respectively, representing mortality in excess of half a million birds. In contrast, declines were less pronounced or absent in these species in regions where the disease was found in intermediate or low incidence. Also, populations of dunnock Prunella modularis, which similarly feeds in gardens, but in which T. gallinae was rarely recorded, did not decline. This is the first trichomonosis epidemic reported in the scientific literature to negatively impact populations of free-ranging non-columbiform species, and such levels of mortality and decline due to an emerging infectious disease are unprecedented in British wild bird populations. This disease emergence event demonstrates the potential for a protozoan parasite to jump avian host taxonomic groups with dramatic effect over a short time period.

Finch trichomonosis, caused by Trichomonas gallinae, emerged in the Canadian Maritime provinces in 2007 and has since caused ongoing mortality in regional purple finch (Carpodacus purpureus) and American goldfinch (Carduelis tristis) populations. Trichomonas gallinae was isolated from (1) finches and rock pigeons (Columbia livia) submitted for post-mortem or live-captured at bird feeding sites experiencing trichomonosis mortality; (2) bird seed at these same sites; and (3) rock pigeons live-captured at known roosts or humanely killed. Isolates were characterized using internal transcribed spacer (ITS) region and iron hydrogenase (Fe-hyd) gene sequences. Two distinct ITS types were found. Type A was identical to the UK finch epidemic strain and was isolated from finches and a rock pigeon with trichomonosis; apparently healthy rock pigeons and finches; and bird seed at an outbreak site. Type B was obtained from apparently healthy rock pigeons. Fe-hyd sequencing revealed six distinct subtypes. The predominant subtype in both finches and the rock pigeon with trichomonosis was identical to the UK finch epidemic strain A1. Single nucleotide polymorphisms in Fe-hyd sequences suggest there is fine-scale variation amongst isolates and that finch trichomonosis emergence in this region may not have been caused by a single spill-over event.

There are about 5000 species of Passeriformes birds, which are half of the extant ones. Their class I MHC molecules are found to be different from all other studied vertebrates, including other bird species; i.e., amino acid residues 10 and 96 are not the seven canonic residues extant in all other vertebrate molecules. Thus, the canonic residues in MHC class I vertebrate molecules are reduced to five. These differences have physical effects in MHC (Major Histocompatibility Complex) class I alpha chain interaction with beta-2-microglobulin but have yet unknown functional effects. Also, introns show specific Passeriformes distinction both in size and invariance. The studies reviewed in this paper on MHC structure have been done in wild birds that cover most of the world’s passerine habitats. In this context, we are going to expose the most commonly occurring bird diseases with the caveat that MHC and disease linkage pathogenesis is not resolved. In addition, this field is poorly studied in birds; however, common bird diseases like malaria and Marek’s disease are linked to MHC. On the other hand, the main established function of MHC molecules is presenting microbial and other antigens to T cells in order to start immune responses, and they also may modulate the immune system through NK receptors and other receptors (non-classical class I MHC molecules). Also, structural and polymorphic differences between classical class I molecules and non-classical class I molecules are at present not clear, and their definition is blurred. These passerine exceptional MHC class I molecules may influence linkage to diseases, transplantation, and other MHC presentation and self-protection functions. Further studies in more Passeriformes species are ongoing and needed.

Birds are highly social and must be paired in order to increase their welfare. Most bird species are monomorphic; therefore, molecular sexing helps provide appropriate welfare for birds. Moreover, early sex determination can be of great value for bird owners. The aim of this study was to demonstrate that sex identification in birds achieved using molecular methods and samples collected via minimally invasive methods is fast, efficient, and accurate. A total of 100 samples (29 paired samples of feathers and oral swabs and 14 tripled samples of feathers, oral swabs, and blood) from 43 birds were included in this study, as follows: wild birds (Falconiformes, Accipitriformes, landfowl—Galliformes, waterfowl—Anseriformes) and companion birds (Passeriformes, Psittaciformes—large-, medium-, and small-sized parrots). Amplification of CHD1-Z and CHD1-W genes was performed via conventional PCR. The results obtained from feathers were compared to those obtained from oral swabs and to those obtained from blood samples, where applicable. The obtained results show that all types of samples can be used for molecular sexing of all studied bird species. To the best of our knowledge, the present study reports, for the first time, molecular sex identification in Red Siskin (Carduelis cucullata) and Goldfinch (Carduelis carduelis major). For higher accuracy, our recommendation is to use minimally invasive samples (oral swabs and feathers) and to test both types of samples for each bird instead of blood samples.

Malaria parasites are highly virulent pathogens which infect a wide range of vertebrates. Despite their importance, the way different hosts control and suppress malaria infections remains poorly understood. With recent developments in next-generation sequencing techniques, however, it is now possible to quantify the response of the entire transcriptome to infections. We experimentally infected Eurasian siskins (Carduelis spinus) with avian malaria parasites (Plasmodium ashfordi), and used high-throughput RNA-sequencing to measure the avian transcriptome in blood collected before infection (day 0), during peak parasitemia (day 21 postinfection), and when parasitemia was decreasing (day 31). We found considerable differences in the transcriptomes of infected and uninfected individuals, with a large number of genes differentially expressed during both peak and decreasing parasitemia stages. These genes were overrepresented among functions involved in the immune system, stress response, cell death regulation, metabolism, and telomerase activity. Comparative analyses of the differentially expressed genes in our study to those found in other hosts of malaria (human and mouse) revealed a set of genes that are potentially involved in highly conserved evolutionary responses to malaria infection. By using RNA-sequencing we gained a more complete view of the host response, and were able to pinpoint not only well-documented host genes but also unannotated genes with clear significance during infection, such as microRNAs. This study shows how the avian blood transcriptome shifts in response to malaria infection, and we believe that it will facilitate further research into the diversity of molecular mechanisms that hosts utilize to fight malaria infections.