Genetic characterization, distribution and prevalence of avian pox and avian malaria in the Berthelot's pipit (Anthus berthelotii) in Macaronesia

Genomic landscapes of divergence among island bird populations: Evidence of parallel adaptation but at different loci?

When populations colonise new environments, they may be exposed to novel selection pressures but also suffer from extensive genetic drift due to founder effects, small population sizes and limited interpopulation gene flow. Genomic approaches enable us to study how these factors drive divergence, and disentangle neutral effects from differentiation at specific loci due to selection. Here, we investigate patterns of genetic diversity and divergence using whole-genome resequencing (>22× coverage) in Berthelot's pipit (Anthus berthelotii), a passerine endemic to the islands of three north Atlantic archipelagos. Strong environmental gradients, including in pathogen pressure, across populations in the species range, make it an excellent system in which to explore traits important in adaptation and/or incipient speciation. First, we quantify how genomic divergence accumulates across the speciation continuum, that is, among Berthelot's pipit populations, between sub species across archipelagos, and between Berthelot's pipit and its mainland ancestor, the tawny pipit (Anthus campestris). Across these colonisation timeframes (2.1 million-ca. 8000 years ago), we identify highly differentiated loci within genomic islands of divergence and conclude that the observed distributions align with expectations for non-neutral divergence. Characteristic signatures of selection are identified in loci associated with craniofacial/bone and eye development, metabolism and immune response between population comparisons. Interestingly, we find limited evidence for repeated divergence of the same loci across the colonisation range but do identify different loci putatively associated with the same biological traits in different populations, likely due to parallel adaptation. Incipient speciation across these island populations, in which founder effects and selective pressures are strong, may therefore be repeatedly associated with morphology, metabolism and immune defence.

Genotype-environment associations reveal genes potentially linked to avian malaria infection in populations of an endemic island bird

Patterns of pathogen prevalence are, at least partially, the result of coevolutionary host-pathogen interactions. Thus, exploring the distribution of host genetic variation in relation to infection by a pathogen within and across populations can provide important insights into mechanisms of host defence and adaptation. Here, we use a landscape genomics approach (Bayenv) in conjunction with genome-wide data (ddRADseq) to test for associations between avian malaria (Plasmodium) prevalence and host genetic variation across 13 populations of the island endemic Berthelot's pipit (Anthus berthelotii). Considerable and consistent spatial heterogeneity in malaria prevalence was observed among populations over a period of 15 years. The prevalence of malaria infection was also strongly positively correlated with pox (Avipoxvirus) prevalence. Multiple host loci showed significant associations with malaria prevalence after controlling for genome-wide neutral genetic structure. These sites were located near to or within genes linked to metabolism, stress response, transcriptional regulation, complement activity and the inflammatory response, many previously implicated in vertebrate responses to malarial infection. Our findings identify diverse genes - not just limited to the immune system - that may be involved in host protection against malaria and suggest that spatially variable pathogen pressure may be an important evolutionary driver of genetic divergence among wild animal populations, such as Berthelot's pipit. Furthermore, our data indicate that spatio-temporal variation in multiple different pathogens (e.g. malaria and pox in this case) may have to be studied together to develop a more holistic understanding of host pathogen-mediated evolution.

A novel pathogenic avipoxvirus infecting oriental turtle dove (Streptopelia orientalis) in China shows a high genomic and evolutionary proximity with the pigeon avipoxviruses isolated globally

Avipoxviruses are considered as significant viral pathogen infecting a wide range of domestic and wild bird species globally, yet the majority of avipoxviruses that infect the wild bird species remain uncharacterized and their genetic diversities remain unclear. In this study, we present a novel pathogenic avipoxvirus isolated from the cutaneous pox lesions of a wild oriental turtle dove (Streptopelia orientalis), tentatively named as turtle dovepox virus (TDPV). The avipoxvirus was isolated by using the chorioallantoic membranes of specific pathogen-free chicken embryos which showed characteristic focal pock lesions, followed by cytopathic effects in host cells infected with oriental turtle dovepox virus. An effort in sequencing the whole genome of the poxvirus using next-generation sequencing was given, and the first whole genome sequence of TDPV was obtained. The TDPV genome was 281,386 bp in length and contained 380 predicted open reading frames (ORFs). While 336 of the predicted ORFs showed homology to other characterized avipoxviruses, the other 44 ORFs were unique. Subsequent phylogenetic analyses showed that the novel TDPV shared the closest genetic evolutionary linkage with the avipoxviruses isolated from pigeon in South Africa and India, of which the TDPV genome had the highest sequence similarity (92.5%) with South African pigeonpox virus (FeP2). In conclusion, the sequenced TDPV is significantly different from any other avipoxviruses isolated from avian or other natural host species considering genomic architecture and observed sequence similarity index. Thus, it likely should be considered a separate species. IMPORTANCE Over the past few decades, avipoxviruses have been found in a number of wild bird species including the oriental turtle dove. However, there is no whole genome sequence information on avipoxviruses isolated from oriental turtle dove, leaving us unclear about the evolutionary linkage of avipoxviruses in oriental turtle dove and other wild bird species. Thus, we believe that our study makes a significant contribution because it is the first report of the whole genome sequence of TDPV isolated from a wild oriental turtle dove, which enriches the genomic information of the genus Avipoxvirus, furthermore, contributes to tracking the genetic evolution of avipoxviruses-infected oriental turtle dove species.

Runs of homozygosity reveal past bottlenecks and contemporary inbreeding across diverging populations of an island-colonizing bird

Genomes retain evidence of the demographic history and evolutionary forces that have shaped populations and drive speciation. Across island systems, contemporary patterns of genetic diversity reflect population demography, including colonization events, bottlenecks, gene flow and genetic drift. Here, we investigate genome-wide diversity and the distribution of runs of homozygosity (ROH) using whole-genome resequencing of individuals (>22× coverage) from six populations across three archipelagos of Berthelot's pipit (Anthus berthelotii)-a passerine that has recently undergone island speciation. We show the most dramatic reduction in diversity occurs between the mainland sister species (the tawny pipit) and Berthelot's pipit and is lowest in the populations that have experienced sequential bottlenecks (i.e., the Madeiran and Selvagens populations). Pairwise sequential Markovian coalescent (PSMC) analyses estimated that Berthelot's pipit diverged from its sister species ~2 million years ago, with the Madeiran archipelago founded 50,000 years ago, and the Selvagens colonized 8000 years ago. We identify many long ROH (>1 Mb) in these most recently colonized populations. Population expansion within the last 100 years may have eroded long ROH in the Madeiran archipelago, resulting in a prevalence of short ROH (<1 Mb). However, the extensive long and short ROH detected in the Selvagens suggest strong recent inbreeding and bottleneck effects, with as much as 38% of the autosomes consisting of ROH >250 kb. These findings highlight the importance of demographic history, as well as selection and genetic drift, in shaping contemporary patterns of genomic diversity across diverging populations.

Genomic associations with poxvirus across divergent island populations in Berthelot's pipit

Understanding the mechanisms and genes that enable animal populations to adapt to pathogens is important from an evolutionary, health and conservation perspective. Berthelot's pipit (Anthus berthelotii) experiences extensive and consistent spatial heterogeneity in avian pox infection pressure across its range of island populations, thus providing an excellent system with which to examine how pathogen-mediated selection drives spatial variation in immunogenetic diversity. Here we test for evidence of genetic variation associated with avian pox at both an individual and population-level. At the individual level, we find no evidence that variation in MHC class I and TLR4 (both known to be important in recognising viral infection) was associated with pox infection within two separate populations. However, using genotype-environment association (Bayenv) in conjunction with genome-wide (ddRAD-seq) data, we detected strong associations between population-level avian pox prevalence and allele frequencies of single nucleotide polymorphisms (SNPs) at a number of sites across the genome. These sites were located within genes involved in cellular stress signalling and immune responses, many of which have previously been associated with responses to viral infection in humans and other animals. Consequently, our analyses indicates that pathogen-mediated selection may play a role in shaping genomic variation among relatively recently colonised island bird populations and highlights the utility of genotype-environment associations for identifying candidate genes potentially involved in host-pathogen interactions.

Molecular Detection of Avipoxvirus in Wild Birds in Central Italy

Simple Summary

Avipoxviruses (APVs) are responsible for diseases in domestic and wild birds. Currently, the disease in domestic animals is under control in many Countries by biosafety and vaccination. In wild birds, small disease events are frequently reported worldwide, but large outbreaks are generally rare. Nevertheless, some aspects of the epidemiology of these viruses are still unclear. In this study, we explored, through molecular investigations, the diffusion of APVs among wild birds, of different orders and species, without typical macroscopic lesions. A high percentage (43.33%) of positive specimens was detected, suggesting high diffusion of the viruses and a possible role of avian wildlife as a reservoir. Aquatic birds, mainly Anseriformes, were more often infected, probably in relation to the environment where they live; in fact, APVs are frequently transmitted by mosquitos, particularly abundant in humid areas.

Abstract

Avipoxviruses (APVs) are important pathogens of both domestic and wild birds. The associated disease is characterized by skin proliferative lesions in the cutaneous form or by lesions of the first digestive and respiratory tracts in the diphtheritic form. Previous studies investigated these infections in symptomatic wild birds worldwide, including Italy, but data about the circulation of APVs in healthy avian wildlife are not available. The present study tested spleen samples from 300 wild birds without typical lesions to detect Avipoxvirus DNA. Overall, 43.33% of the samples scored positive. Aquatic birds were more frequently infected (55.42%) than other animals (26.40%), and in Anseriformes, high positivity was found (52.87%). The obtained results suggest that wild birds could be asymptomatic carriers of Avipoxviruses, opening new possible epidemiological scenarios.

Prevalence and Genetic Diversity of Avian Haemosporidian Parasites in Southern Iran

Avian haemosporidians are widespread and diverse and are classified in the genera Plasmodium, Haemoproteus, Leucocytozoon, and Fallisia. These species are known to cause haemosporidiosis and decreased fitness of their hosts. Despite the high diversity of habitats and animal species in Iran, only few studies have addressed avian haemosporidians in this geographic area. This study was performed in the south and southeast of Iran during the bird breeding seasons in 2017 and 2018, with the aim to partly fill in this gap. Blood samples of 237 passerine birds belonging to 41 species and 20 families were collected. Parasite infections were identified using a nested PCR protocol targeting a 479-base-pair fragment of the mitochondrial cytochrome b (cytb) gene of Haemoproteus, Plasmodium and Leucocytozoon species. The overall prevalence of haemosporidian parasites was 51.1%, and 55 different lineages were identified, of which 15 cytb lineages were new globally. The lineages of Haemoproteus predominated (63.6% of all detected lineages), followed by Leucocytozoon and Plasmodium. Nineteen new host records of haemosporidian cytb lineages were identified, and the majority of them were found in resident bird species, indicating local transmission. Thirteen co-infections (9.8% of infected individuals) of Haemoproteus and Leucocytozoon parasites in seven host species were observed. This study shows the presence of active local transmission of parasites to resident bird species in the southeast of Iran and contributes to the knowledge on haemosporidian parasite biodiversity in this poorly studied region of the world.

Genomic Characterisation of a Novel Avipoxvirus Isolated from an Endangered Northern Royal Albatross (Diomedea sanfordi)

Marine bird populations have been declining globally with the factors driving this decline not fully understood. Viral diseases, including those caused by poxviruses, are a concern for endangered seabird species. In this study we have characterised a novel avipoxvirus, tentatively designated albatrosspox virus (ALPV), isolated from a skin lesion of an endangered New Zealand northern royal albatross (Diomedea sanfordi). The ALPV genome was 351.9 kbp in length and contained 336 predicted genes, seven of which were determined to be unique. The highest number of genes (313) in the ALPV genome were homologs of those in shearwaterpox virus 2 (SWPV2), while a further 10 were homologs to canarypox virus (CNPV) and an additional six to shearwaterpox virus 1 (SWPV1). Phylogenetic analyses positioned the ALPV genome within a distinct subclade comprising recently isolated avipoxvirus genome sequences from shearwater, penguin and passerine bird species. This is the first reported genome sequence of ALPV from a northern royal albatross and will help to track the evolution of avipoxvirus infections in this endangered species.

A Review on the Prevalence of Poxvirus Disease in Free-Living and Captive Wild Birds

Avian pox is a widespread infection in birds caused by genus Avipoxvirus pathogens. It is a noteworthy, potentially lethal disease to wild and domestic hosts. It can produce two different conditions: cutaneous pox, and diphtheritic pox. Here, we carry out an exhaustive review of all cases of avian pox reported from wild birds to analyze the effect and distribution in different avian species. Avian poxvirus strains have been detected in at least 374 wild bird species, a 60% increase on a 1999 review on avian pox hosts. We also analyze epizootic cases and if this disease contributes to wild bird population declines. We frequently observe very high prevalence in wild birds in remote island groups, e.g., Hawaii, Galapagos, etc., representing a major risk for the conservation of their unique endemic avifauna. However, the difference in prevalence between islands and continents is not significant given the few available studies. Morbidity and mortality can also be very high in captive birds, due to high population densities. However, despite the importance of the disease, the current detection rate of new Avipoxvirus strains suggests that diversity is incomplete for this group, and more research is needed to clarify its real extent, particularly in wild birds.

Genomic Characterisation of a Novel Avipoxvirus Isolated from an Endangered Yellow-Eyed Penguin (Megadyptes antipodes)

Emerging viral diseases have become a significant concern due to their potential consequences for animal and environmental health. Over the past few decades, it has become clear that viruses emerging in wildlife may pose a major threat to vulnerable or endangered species. Diphtheritic stomatitis, likely to be caused by an avipoxvirus, has been recognised as a significant cause of mortality for the endangered yellow-eyed penguin (Megadyptes antipodes) in New Zealand. However, the avipoxvirus that infects yellow-eyed penguins has remained uncharacterised. Here, we report the complete genome of a novel avipoxvirus, penguinpox virus 2 (PEPV2), which was derived from a virus isolate obtained from a skin lesion of a yellow-eyed penguin. The PEPV2 genome is 349.8 kbp in length and contains 327 predicted genes; five of these genes were found to be unique, while a further two genes were absent compared to shearwaterpox virus 2 (SWPV2). In comparison with penguinpox virus (PEPV) isolated from an African penguin, there was a lack of conservation within the central region of the genome. Subsequent phylogenetic analyses of the PEPV2 genome positioned it within a distinct subclade comprising the recently isolated avipoxvirus genome sequences from shearwater, canary, and magpie bird species, and demonstrated a high degree of sequence similarity with SWPV2 (96.27%). This is the first reported genome sequence of PEPV2 from a yellow-eyed penguin and will help to track the evolution of avipoxvirus infections in this rare and endangered species.

Molecular characterisation of a novel pathogenic avipoxvirus from an Australian passerine bird, mudlark (Grallina cyanoleuca)

Avipoxviruses have been recognised as significant pathogens in the conservation of numerous bird species. However, the vast majority of the avipoxviruses that infect wild birds remain uncharacterised. Here, we characterise a novel avipoxvirus, mudlarkpox virus (MLPV) isolated from an Australian passerine bird, mudlark (Grallina cyanoleuca). In this study, tissues with histopathologically confirmed lesions consistent with avian pox were used for transmission electron microscopy, and showed characteristic ovoid to brick-shaped virions, indicative of infectious particles. The MLPV genome was >342.7 Kbp in length and contained six predicted novel genes and a further six genes were missing compared to shearwaterpox virus-2 (SWPV-2). Subsequent phylogenetic analyses of the MLPV genome positioned the virus within a distinct subclade also containing recently characterised avipoxvirus genomes from shearwater, canary and magpie bird species, and demonstrated a high degree of sequence similarity with SWPV-2 (94.92%).

Adaptive landscape genetics and malaria across divergent island bird populations

Environmental conditions play a major role in shaping the spatial distributions of pathogens, which in turn can drive local adaptation and divergence in host genetic diversity. Haemosporidians, such as Plasmodium (malaria), are a strong selective force, impacting survival and fitness of hosts, with geographic distributions largely determined by habitat suitability for their insect vectors. Here, we have tested whether patterns of fine-scale local adaptation to malaria are replicated across discrete, ecologically differing island populations of Berthelot's pipits Anthus berthelotii. We sequenced TLR4, an innate immunity gene that is potentially under positive selection in Berthelot's pipits, and two SNPs previously identified as being associated with malaria infection in a genome-wide association study (GWAS) in Berthelot's pipits in the Canary Islands. We determined the environmental predictors of malaria infection, using these to estimate variation in malaria risk on Porto Santo, and found some congruence with previously identified environmental risk factors on Tenerife. We also found a negative association between malaria infection and a TLR4 variant in Tenerife. In contrast, one of the GWAS SNPs showed an association with malaria risk in Porto Santo, but in the opposite direction to that found in the Canary Islands GWAS. Together, these findings suggest that disease-driven local adaptation may be an important factor in shaping variation among island populations.

Genomic associations with bill length and disease reveal drift and selection across island bird populations

Island species provide excellent models for investigating how selection and drift operate in wild populations, and for determining how these processes act to influence local adaptation and speciation. Here, we examine the role of selection and drift in shaping genomic and phenotypic variation across recently separated populations of Berthelot's pipit (Anthus berthelotii), a passerine bird endemic to three archipelagos in the Atlantic. We first characterized genetic diversity and population structuring that supported previous inferences of a history of recent colonizations and bottlenecks. We then tested for regions of the genome associated with the ecologically important traits of bill length and malaria infection, both of which vary substantially across populations in this species. We identified a SNP associated with variation in bill length among individuals, islands, and archipelagos; patterns of variation at this SNP suggest that both phenotypic and genotypic variation in bill length is largely shaped by founder effects. Malaria was associated with SNPs near/within genes involved in the immune response, but this relationship was not consistent among archipelagos, supporting the view that disease resistance is complex and rapidly evolving. Although we found little evidence for divergent selection at candidate loci for bill length and malaria resistance, genome scan analyses pointed to several genes related to immunity and metabolism as having important roles in divergence and adaptation. Our findings highlight the utility and challenges involved with combining association mapping and population genetic analysis in nonequilibrium populations, to disentangle the effects of drift and selection on shaping genotypes and phenotypes.

Factors governing the prevalence and richness of avian haemosporidian communities within and between temperate mountains

Mountains are well-suited systems to disentangle the factors driving distribution of parasites due to their heterogeneity of climatic and habitat conditions. However, the information about the relative importance of environmental factors governing the distribution of avian haemosporidians on temperate mountains is very limited. The main goal of the present study is to identify the factors determining prevalence and richness in avian haemosporidians (Plasmodium, Haemoproteus and Leucocytozoon) at the community level along elevational gradients on two mountain ranges located around the northern and southern limits of the Iberian Peninsula (Spain). We used samples from 68 avian species and 1,460 breeding individuals caught over widespread woodland and open habitats. Our findings confirmed the importance of climatic variables explaining prevalence and richness on Iberian mountains. However, landscape variables and other factors named host richness and migration behaviour explained more variation than climatic ones. Plasmodium genus preferred open and warm habitats. Water sources were also important for the southern but not for the northern mountain. Haemoproteus and Leucocytozoon showed affinities for woodland areas. Climatic conditions for Haemoproteus and Leucocytozoon were dependent on the mountain range suggesting some adaptation of avian haemosporidian and their invertebrate vectors to the climatic particularities of both mountain massifs. In contrast to Plasmodium and Haemoproteus genera, Leucocytozoon prevalence and richness values were significantly higher in the southern mountain range. Overall, our findings at the community level has enriched the relative weight and effect direction of environmental factors governing the distribution and prevalence of the avian haemosporidian community. Also, our results provide a caution message about the precision of predictive models on parasite distributions based on climatic variables, since such predictions could overestimate the effect of climate change scenarios on the transmission of the haemosporidians.

Genomic characterization of two novel pathogenic avipoxviruses isolated from pacific shearwaters (Ardenna spp.)

Background

Over the past 20 years, many marine seabird populations have been gradually declining and the factors driving this ongoing deterioration are not always well understood. Avipoxvirus infections have been found in a wide range of bird species worldwide, however, very little is known about the disease ecology of avian poxviruses in seabirds. Here we present two novel avipoxviruses from pacific shearwaters (Ardenna spp), one from a Flesh-footed Shearwater (A. carneipes) (SWPV-1) and the other from a Wedge-tailed Shearwater (A. pacificus) (SWPV-2).

Results

Epidermal pox lesions, liver, and blood samples were examined from A. carneipes and A. pacificus of breeding colonies in eastern Australia. After histopathological confirmation of the disease, PCR screening was conducted for avipoxvirus, circovirus, reticuloendotheliosis virus, and fungal agents. Two samples that were PCR positive for poxvirus were further assessed by next generation sequencing, which yielded complete Shearwaterpox virus (SWPV) genomes from A. pacificus and A. carneipes, both showing the highest degree of similarity with Canarypox virus (98% and 67%, respectively). The novel SWPV-1 complete genome from A. carneipes is missing 43 genes compared to CNPV and contains 4 predicted genes which are not found in any other poxvirus, whilst, SWPV-2 complete genome was deemed to be missing 18 genes compared to CNPV and a further 15 genes significantly fragmented as to probably cause them to be non-functional.

Conclusion

These are the first avipoxvirus complete genome sequences that infect marine seabirds. In the comparison of SWPV-1 and −2 to existing avipoxvirus sequences, our results indicate that the SWPV complete genome from A. carneipes (SWPV-1) described here is not closely related to any other avipoxvirus genome isolated from avian or other natural host species, and that it likely should be considered a separate species.

Electronic supplementary material

The online version of this article (doi:10.1186/s12864-017-3680-z) contains supplementary material, which is available to authorized users.

Prevalence and Genetic Diversity of Avipoxvirus in House Sparrows in Spain

Avipoxvirus (APV) is a fairly common virus affecting birds that causes morbidity and mortality in wild and captive birds. We studied the prevalence of pox-like lesions and genetic diversity of APV in house sparrows (Passer domesticus) in natural, agricultural and urban areas in southern Spain in 2013 and 2014 and in central Spain for 8 months (2012-2013). Overall, 3.2% of 2,341 house sparrows visually examined in southern Spain had cutaneous lesions consistent with avian pox. A similar prevalence (3%) was found in 338 birds from central Spain. Prevalence was higher in hatch-year birds than in adults. We did not detect any clear spatial or temporal patterns of APV distribution. Molecular analyses of poxvirus-like lesions revealed that 63% of the samples were positive. Molecular and phylogenetic analyses of 29 DNA sequences from the fpv167 gene, detected two strains belonging to the canarypox clade (subclades B1 and B2) previously found in Spain. One of them appears predominant in Iberia and North Africa and shares 70% similarity to fowlpox and canarypox virus. This APV strain has been identified in a limited number of species in the Iberian Peninsula, Morocco and Hungary. The second one has a global distribution and has been found in numerous wild bird species around the world. To our knowledge, this represents the largest study of avian poxvirus disease in the broadly distributed house sparrow and strongly supports the findings that Avipox prevalence in this species in South and central Spain is moderate and the genetic diversity low.

The Strait of Gibraltar poses an effective barrier to host-specialised but not to host-generalised lineages of avian Haemosporidia

One of the major concerns with ongoing environmental global change is the ability of parasites to shift their distribution (both geographically and across hosts) and to increase in virulence. To understand the structure, diversity and connectivity of parasite communities across the Mediterranean Sea, we used avian haemosporidian communities associated with forest birds of northwestern Africa and northwestern Iberia as a model system. We characterised host specificity of lineages and tested whether host generalists are more likely to cross the biogeographic barrier imposed by the Strait of Gibraltar than host specialists. We sampled 321 birds of 43 species in northwestern Africa and 735 birds of 49 species in northwestern Iberia. Using a PCR-based approach to amplify Plasmodium, Haemoproteus and Leucocytozoon parasites, we retrieved 969 sequences representing 200 unique cytochrome-b lineages. Haemosporidians infected a significantly higher proportion of birds in northwestern Africa (78.5%) than in northwestern Iberia (50.5%). Relative diversity of different haemosporidian genera did not differ between our study areas, but Plasmodium was overrepresented among individual infections in northwestern Iberia. Haemoproteus and Leucocytozoon lineages were predominantly host-specialised and Plasmodium lineages were host-generalised. The number of regions occupied by lineages was significantly associated with their host specificity and abundance. These data are consistent with the positive abundance-occupancy relationship and patterns of host specificity among different haemosporidian genera observed in other studies.

Low prevalence of blood parasites in a long-distance migratory raptor: the importance of host habitat

BACKGROUND

The low prevalence of blood parasites in some bird species may be related to the habitats they frequent, the inexistence of the right host-parasite assemblage or the immunological capacity of the host. Here, we assess the parasite load of breeding populations of Eleonora's falcon (Falco eleonorae), a medium-sized long-distance migratory raptor that breeds on small isolated islets throughout the Mediterranean basin and overwinters in inland Madagascar.

METHODS

We examined the prevalence and genetic diversity of the blood parasites belonging to the genera Plasmodium, Haemoproteus and Leucocytozoon in Eleonora's falcon nestlings from five colonies and in adults from two colonies from nesting sites distributed throughout most of the species' breeding range.

RESULTS

None of the 282 nestlings analysed were infected by blood parasites; on the other hand, the lineages of Plasmodium, Haemoproteus and Leucocytozoon were all found to infect adults. Our results support the idea of no local transmission of vector-borne parasites in marine habitats. Adult Eleonora's falcons thus may be infected by parasites when on migration or in their wintering areas.

CONCLUSION

The characteristics of marine environments with a lack of appropriate vectors may thus be the key factor determining the absence of local transmission of blood parasites. By comparing the parasite lineages isolated in this species with those previously found in other birds we were able to infer the most likely areas for the transmission of the various parasite lineages.

Worldwide phylogenetic relationship of avian poxviruses

Poxvirus infections have been found in 230 species of wild and domestic birds worldwide in both terrestrial and marine environments. This ubiquity raises the question of how infection has been transmitted and globally dispersed. We present a comprehensive global phylogeny of 111 novel poxvirus isolates in addition to all available sequences from GenBank. Phylogenetic analysis of the Avipoxvirus genus has traditionally relied on one gene region (4b core protein). In this study we expanded the analyses to include a second locus (DNA polymerase gene), allowing for a more robust phylogenetic framework, finer genetic resolution within specific groups, and the detection of potential recombination. Our phylogenetic results reveal several major features of avipoxvirus evolution and ecology and propose an updated avipoxvirus taxonomy, including three novel subclades. The characterization of poxviruses from 57 species of birds in this study extends the current knowledge of their host range and provides the first evidence of the phylogenetic effect of genetic recombination of avipoxviruses. The repeated occurrence of avian family or order-specific grouping within certain clades (e.g., starling poxvirus, falcon poxvirus, raptor poxvirus, etc.) indicates a marked role of host adaptation, while the sharing of poxvirus species within prey-predator systems emphasizes the capacity for cross-species infection and limited host adaptation. Our study provides a broad and comprehensive phylogenetic analysis of the Avipoxvirus genus, an ecologically and environmentally important viral group, to formulate a genome sequencing strategy that will clarify avipoxvirus taxonomy.

Emergence of a novel avian pox disease in British tit species

Avian pox is a viral disease with a wide host range. In Great Britain, avian pox in birds of the Paridae family was first diagnosed in a great tit (Parus major) from south-east England in 2006. An increasing number of avian pox incidents in Paridae have been reported each year since, indicative of an emergent infection. Here, we utilise a database of opportunistic reports of garden bird mortality and morbidity to analyse spatial and temporal patterns of suspected avian pox throughout Great Britain, 2006-2010. Reports of affected Paridae (211 incidents) outnumbered reports in non-Paridae (91 incidents). The majority (90%) of Paridae incidents involved great tits. Paridae pox incidents were more likely to involve multiple individuals (77.3%) than were incidents in non-Paridae hosts (31.9%). Unlike the small wart-like lesions usually seen in non-Paridae with avian pox in Great Britain, lesions in Paridae were frequently large, often with an ulcerated surface and caseous core. Spatial analyses revealed strong clustering of suspected avian pox incidents involving Paridae hosts, but only weak, inconsistent clustering of incidents involving non-Paridae hosts. There was no spatial association between Paridae and non-Paridae incidents. We documented significant spatial spread of Paridae pox from an origin in south-east England; no spatial spread was evident for non-Paridae pox. For both host clades, there was an annual peak of reports in August/September. Sequencing of the avian poxvirus 4b core protein produced an identical viral sequence from each of 20 great tits tested from Great Britain. This sequence was identical to that from great tits from central Europe and Scandinavia. In contrast, sequence variation was evident amongst virus tested from 17 non-Paridae hosts of 5 species. Our findings show Paridae pox to be an emerging infectious disease in wild birds in Great Britain, apparently originating from viral incursion from central Europe or Scandinavia.

Epidemiology of the emergent disease Paridae pox in an intensively studied wild bird population

Paridae pox, a novel avipoxvirus infection, has recently been identified as an emerging infectious disease affecting wild tit species in Great Britain. The incursion of Paridae pox to a long-term study site where populations of wild tits have been monitored in detail for several decades provided a unique opportunity to obtain information on the local-scale epidemiological characteristics of this novel infection during a disease outbreak. Using captures of >8000 individual birds, we show that, within two years of initial emergence, Paridae pox had become established within the population of great tits (Parus major) reaching relatively high peak prevalence (10%), but was far less prevalent (<1%) in sympatric populations of several other closely related, abundant Paridae species. Nonlinear smoothing models revealed that the temporal pattern of prevalence among great tits was characterised by within-year fluctuations indicative of seasonal forcing of infection rates, which was likely driven by multiple environmental and demographic factors. There was individual heterogeneity in the course of infection and, although recovery was possible, diseased individuals were far less likely to be recaptured than healthy individuals, suggesting a survival cost of infection. This study demonstrates the value of long-term monitoring for obtaining key epidemiological data necessary to understand disease dynamics, spread and persistence in natural populations.

Patterns in avian malaria at founder and source populations of an endemic New Zealand passerine

Significant progress in our understanding of disease transmission in the wild can be made by examining variation in host-parasite-vector interactions after founder events of the host. This study is the first to document patterns in avian malaria, Plasmodium spp., infecting an endemic New Zealand passerine, Anthornis melanura, at multiple-host subpopulations simultaneously. We assess the Beaudoin hypothesis of bimodal seasonality and use AIC model selection to determine host factors associated with disease prevalence. We had the rare opportunity to test the enemy release hypothesis (ERH) after a recent colonisation event of the bellbird host. Four Plasmodium species were found to infect bellbirds. Temporal patterns of three exotic parasite lineages, including GRW06 Plasmodium (Huffia) elongatum, SYAT05 Plasmodium (Novyella) vaughani and a Plasmodium (Haemamoeba) relictum, were sporadic with low prevalence year round. The fourth species was an endemic parasite, an unresolved Plasmodium (Novyella) sp. here called ANME01, which exhibited a strong winter peak at the source subpopulations possibly indicating greater immune stressors at the densely populated source site. At the colonies, we observed bimodal seasonality in the prevalence of ANME01 with autumn and spring peaks. These infection peaks were male-biased, and the amplitude of sex bias was more pronounced at the newer colony perhaps due to increased seasonal competition resulting from territory instability. We observed a decrease in parasite species diversity and increase in body condition from source to founder sites, but statistical differences in the direct relationship between body condition and malaria prevalence between source and colony were weak and significant only during winter. Though our data did not strongly support the ERH, we highlight the benefits of 'conspecific release' associated with decreased population density and food competition. Our findings contribute to the identification of ecological and environmental drivers of variability in malaria transmission, which is valuable for predicting the consequences of both natural range expansions, as well as host re-introductions resulting from intensive conservation practices.

Biogeographical patterns and co-occurrence of pathogenic infection across island populations of Berthelot's pipit (Anthus berthelotii)

Pathogens can exert strong selective forces upon host populations. However, before we can make any predictions about the consequences of pathogen-mediated selection, we first need to determine whether patterns of pathogen distribution are consistent over spatiotemporal scales. We used molecular techniques to screen for a variety of blood pathogens (avian malaria, pox and trypanosomes) over a three-year time period across 13 island populations of the Berthelot's pipit (Anthus berthelotii). This species has only recently dispersed across its range in the North Atlantic, with little subsequent migration, providing an ideal opportunity to examine the causes and effects of pathogenic infection in populations in the early stages of differentiation. We screened 832 individuals, and identified two strains of Plasmodium, four strains of Leucocytozoon, and one pox strain. We found strong differences in pathogen prevalence across populations, ranging from 0 to 65%, and while some fluctuations in prevalence occurred, these differences were largely stable over the time period studied. Smaller, more isolated islands harboured fewer pathogen strains than larger, less isolated islands, indicating that at the population level, colonization and extinction play an important role in determining pathogen distribution. Individual-level analyses confirmed the island effect, and also revealed a positive association between Plasmodium and pox infection, which could have arisen due to dual transmission of the pathogens by the same vectors, or because one pathogen lowers resistance to the other. Our findings, combined with an effect of infection on host body condition, suggest that Berthelot's pipits are subject to different levels of pathogen-mediated selection both across and within populations, and that these selective pressures are consistent over time.

The phylogenetic analysis of avipoxvirus in New Zealand

Avipoxvirus is known to be endemic in New Zealand and it is a cause of ongoing mortalities in the endangered black robin and shore plover populations. There is no information on the strains of avipoxvirus occurring in New Zealand and their likely origin or pathogenicity. This study was designed to identify the phylogenetic relationships of pathogenic avipoxvirus strains infecting introduced, native, and endemic bird species in New Zealand. Avipoxvirus 4b core protein gene was detected in tissue samples from 25/48 birds (52.1%) from 15 different species in New Zealand. Bootstrap analysis of avipoxvirus 4b core protein gene revealed that the New Zealand avipoxvirus isolates comprised of three different subclades. The majority of New Zealand avipoxvirus isolates (74%) belonged to A1 subclade which shared 100% genetic similarity with the fowlpox HPB strain. An isolate from a wood-pigeon (kereru) belonged to subclade A3, displaying 100% sequence homology to albatrosspox virus. An additional group, isolated from two shore plovers and one South Island saddleback, grouped within subclade B1 and presented 99% sequence homology to European PM33/2007 and Hawaiian HAAM 22.10H8 isolates. The results suggest that a variety of New Zealand bird species are susceptible to avipoxvirus infection, that there are more than two distinctive avipoxvirus subclades in New Zealand, and that the most prevalent A1 strain may have been introduced to New Zealand through introduced avian hosts such as passerines or poultry.

Goats, birds, and emergent diseases: apparent and hidden effects of exotic species in an island environment

Exotic species can have devastating effects on recipient environments and even lead to the outbreak of emergent diseases. We present here several hidden effects that the introduction of goats has had on the Lesser Short-toed Lark, Calandrella rufescens, the commonest native bird inhabiting the island of Fuerteventura (Canary Islands). Vegetation structure varied with grazing pressure, and indeed, vegetation was all but eradicated from the locality with greatest goat densities, which was also where the lowest density of Lesser Short-toed Larks was recorded. The impact of habitat impoverishment, however, was partially compensated for by changes in the foraging behavior of birds, which benefited from the abundant food provided to goats on farms. Capture-resighting methods showed that birds visiting farms outnumbered the estimates for birds obtained in the surrounding natural habitat, suggesting that there was recruitment from a much larger area. Stable isotope analyses of feathers indicated that island birds feed largely on the maize supplied at goat farms, showing poorer body condition than birds from populations not associated with farms (peninsular Spain and Morocco). Moreover, larks from Fuerteventura had a very high prevalence of poxvirus lesions compared with other bird populations worldwide and may increase the risk of contracting the disease by feeding on farms, where they aggregate and coexist atypically with domestic birds. The island birds also had lower average productivity, which may be the consequence of the emergent disease and/or the poor nutritional state resulting from feeding on a low-protein diet. Diseased and non-diseased birds from Fuerteventura showed similar body condition and annual survival rates. However, the isotopic traces of delta 13C indicate that the diet of diseased birds was more uniform than that of non-diseased birds, being based on food from goat farms. Our results show how the combination of species frequently introduced onto islands (goats, poultry, and associated pathogens) can create ecological traps for native species that are not always easy to identify. Moreover, we stress that nutrition and infectious diseases are important determinants of the well-being and dynamics of animal populations, and thus health research must be included in the design of monitoring programs and conservation strategies.