Publications by authors named "Marcel Klaassen"

72 Publications

An evaluation of machine learning classifiers for next-generation, continuous-ethogram smart trackers.

Mov Ecol 2021 Mar 30;9(1):15. Epub 2021 Mar 30.

Centre for Integrative Ecology, School of Life and Environmental Sciences, Deakin University, Geelong, Victoria, Australia.

Background: Our understanding of movement patterns and behaviours of wildlife has advanced greatly through the use of improved tracking technologies, including application of accelerometry (ACC) across a wide range of taxa. However, most ACC studies either use intermittent sampling that hinders continuity or continuous data logging relying on tracker retrieval for data downloading which is not applicable for long term study. To allow long-term, fine-scale behavioural research, we evaluated a range of machine learning methods for their suitability for continuous on-board classification of ACC data into behaviour categories prior to data transmission.

Methods: We tested six supervised machine learning methods, including linear discriminant analysis (LDA), decision tree (DT), support vector machine (SVM), artificial neural network (ANN), random forest (RF) and extreme gradient boosting (XGBoost) to classify behaviour using ACC data from three bird species (white stork Ciconia ciconia, griffon vulture Gyps fulvus and common crane Grus grus) and two mammals (dairy cow Bos taurus and roe deer Capreolus capreolus).

Results: Using a range of quality criteria, SVM, ANN, RF and XGBoost performed well in determining behaviour from ACC data and their good performance appeared little affected when greatly reducing the number of input features for model training. On-board runtime and storage-requirement tests showed that notably ANN, RF and XGBoost would make suitable on-board classifiers.

Conclusions: Our identification of using feature reduction in combination with ANN, RF and XGBoost as suitable methods for on-board behavioural classification of continuous ACC data has considerable potential to benefit movement ecology and behavioural research, wildlife conservation and livestock husbandry.
View Article and Find Full Text PDF

Download full-text PDF

Source
http://dx.doi.org/10.1186/s40462-021-00245-xDOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC8011142PMC
March 2021

Reassortment and Persistence of Influenza A Viruses from Diverse Geographic Origins within Australian Wild Birds: Evidence from a Small, Isolated Population of Ruddy Turnstones.

J Virol 2021 04 12;95(9). Epub 2021 Apr 12.

Department of Microbiology, Biomedicine Discovery Institute, Monash University, Clayton, Victoria Australia

Australian lineages of avian influenza A viruses (AIVs) are thought to be phylogenetically distinct from those circulating in Eurasia and the Americas, suggesting the circulation of endemic viruses seeded by occasional introductions from other regions. However, processes underlying the introduction, evolution and maintenance of AIVs in Australia remain poorly understood. Waders (order Charadriiformes, family Scolopacidae) may play a unique role in the ecology and evolution of AIVs, particularly in Australia, where ducks, geese, and swans (order Anseriformes, family Anatidae) rarely undertake intercontinental migrations. Across a 5-year surveillance period (2011 to 2015), ruddy turnstones () that "overwinter" during the Austral summer in southeastern Australia showed generally low levels of AIV prevalence (0 to 2%). However, in March 2014, we detected AIVs in 32% (95% confidence interval [CI], 25 to 39%) of individuals in a small, low-density, island population 90 km from the Australian mainland. This epizootic comprised three distinct AIV genotypes, each of which represent a unique reassortment of Australian-, recently introduced Eurasian-, and recently introduced American-lineage gene segments. Strikingly, the Australian-lineage gene segments showed high similarity to those of H10N7 viruses isolated in 2010 and 2012 from poultry outbreaks 900 to 1,500 km to the north. Together with the diverse geographic origins of the American and Eurasian gene segments, these findings suggest extensive circulation and reassortment of AIVs within Australian wild birds over vast geographic distances. Our findings indicate that long-term surveillance in waders may yield unique insights into AIV gene flow, especially in geographic regions like Oceania, where Anatidae species do not display regular inter- or intracontinental migration. High prevalence of avian influenza viruses (AIVs) was detected in a small, low-density, isolated population of ruddy turnstones in Australia. Analysis of these viruses revealed relatively recent introductions of viral gene segments from both Eurasia and North America, as well as long-term persistence of introduced gene segments in Australian wild birds. These data demonstrate that the flow of viruses into Australia may be more common than initially thought and that, once introduced, these AIVs have the potential to be maintained within the continent. These findings add to a growing body of evidence suggesting that Australian wild birds are unlikely to be ecologically isolated from the highly pathogenic H5Nx viruses circulating among wild birds throughout the Northern Hemisphere.
View Article and Find Full Text PDF

Download full-text PDF

Source
http://dx.doi.org/10.1128/JVI.02193-20DOI Listing
April 2021

Microbial symbiosis and coevolution of an entire clade of ancient vertebrates: the gut microbiota of sea turtles and its relationship to their phylogenetic history.

Anim Microbiome 2020 May 7;2(1):17. Epub 2020 May 7.

School of Biological Sciences, Monash University, Wellington Rd, Clayton, Victoria, 3800, Australia.

Background: The microbiota plays a critical role in host homeostasis and has been shown to be a major driving force in host evolution. However, our understanding of these important relationships is hampered by a lack of data for many species, and by significant gaps in sampling of the evolutionary tree. In this investigation we improve our understanding of the host-microbiome relationship by obtaining samples from all seven extant species of sea turtle, and correlate microbial compositions with host evolutionary history.

Results: Our analysis shows that the predominate phyla in the microbiota of nesting sea turtles was Proteobacteria. We also demonstrate a strong relationship between the bacterial phyla SR1 and sea turtle phylogeny, and that sea turtle microbiotas have changed very slowly over time in accordance with their similarly slow phenotypic changes.

Conclusions: This is one of the most comprehensive microbiota studies to have been performed in a single clade of animals and further improves our knowledge of how microbial populations have influenced vertebrate evolution.
View Article and Find Full Text PDF

Download full-text PDF

Source
http://dx.doi.org/10.1186/s42523-020-00034-8DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC7807503PMC
May 2020

Metagenomic characterisation of additional and novel avian viruses from Australian wild ducks.

Sci Rep 2020 12 17;10(1):22284. Epub 2020 Dec 17.

Geelong Centre for Emerging Infectious Diseases, Geelong, VIC, 3220, Australia.

Birds, notably wild ducks, are reservoirs of pathogenic and zoonotic viruses such as influenza viruses and coronaviruses. In the current study, we used metagenomics to detect and characterise avian DNA and RNA viruses from wild Pacific black ducks, Chestnut teals and Grey teals collected at different time points from a single location. We characterised a likely new species of duck aviadenovirus and a novel duck gyrovirus. We also report what, to the best of our knowledge, is the first finding of an avian orthoreovirus from Pacific black ducks and a rotavirus F from Chestnut teals. Other viruses characterised from the samples from these wild ducks belong to the virus families Astroviridae, Caliciviridae and Coronaviridae. Some of the viruses may have potential cross-species transmissibility, while others indicated a wide genetic diversity of duck viruses within a genus. The study also showed evidence of potential transmission of viruses along the East Asian-Australasian Flyway; potentially facilitated by migrating shorebirds. The detection and characterisation of several avian viruses not previously described, and causing asymptomatic but potentially also symptomatic infections suggest the need for more virus surveillance studies for pathogenic and potential zoonotic viruses in wildlife reservoirs.
View Article and Find Full Text PDF

Download full-text PDF

Source
http://dx.doi.org/10.1038/s41598-020-79413-9DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC7747739PMC
December 2020

Migration strategy as an indicator of resilience to change in two shorebird species with contrasting population trajectories.

J Anim Ecol 2020 Nov 24. Epub 2020 Nov 24.

Centre for Integrative Ecology, Deakin University, Melbourne, Vic., Australia.

Many migratory birds are declining worldwide. In line with the general causes for the global biodiversity crisis, habitat loss, pollution, hunting, over-exploitation and climate change are thought to be at the basis of these population declines. Long-distance migrants seem especially vulnerable to rapid anthropogenic change, yet, the rate of decline across populations and species varies greatly within flyways. We hypothesize that differences in migration strategy, and notably stopover-site use, may be at the basis of these variations in resilience to global change. By identifying and comparing the migration strategies of two very closely related shorebird species, the Curlew sandpiper Calidris ferruginea and the Red-necked stint Calidris ruficollis, migrating from the same non-breeding site in Australia to similar breeding sites in the high Russian Arctic, we aimed to explain why these two species express differential resilience to rapid changes within their flyway resulting in different population trajectories in recent times. Based on 13 Curlew sandpiper and 16 Red-necked stint tracks from light-level geolocator tags, we found that individual Curlew sandpipers make use of fewer stopover areas along the flyway compared to Red-necked stints. Furthermore, and notably during northward migration, Curlew sandpipers have a higher dependency on fewer sites, both in terms of the percentage of individuals visiting key stopover sites and the relative time spent at those sites. While Curlew sandpipers rely mainly on the Yellow Sea region, which has recently experienced a sharp decline in suitable habitat, Red-necked stints make use of additional sites and spread their relative time en-route across sites more evenly. Our results indicate that differential migration strategies may explain why Curlew sandpipers within the East Asian-Australasian Flyway are declining rapidly (9.5%-5.5% per year) while Red-necked stints remain relatively stable (-3.1%-0%). We consider that more generally, the number of sites per individual and among a population, the spatial distribution across the flyway, as well as the relationship between the time spent over sites may prove to be key variables explaining populations and species' differential resilience to environmental change.
View Article and Find Full Text PDF

Download full-text PDF

Source
http://dx.doi.org/10.1111/1365-2656.13393DOI Listing
November 2020

Metagenomic characterisation of avian parvoviruses and picornaviruses from Australian wild ducks.

Sci Rep 2020 07 30;10(1):12800. Epub 2020 Jul 30.

Geelong Centre for Emerging Infectious Diseases, Geelong, VIC, 3220, Australia.

Ducks can shed and disseminate viruses and thus play a role in cross-species transmission. In the current study, we detected and characterised various avian parvoviruses and picornaviruses from wild Pacific black ducks, Chestnut teals, Grey teals and Wood ducks sampled at multiple time points from a single location using metagenomics. We characterised 46 different avian parvoviruses belonging to three different genera Dependoparvovirus, Aveparvovirus and Chaphamaparvovirus, and 11 different avian picornaviruses tentatively belonging to four different genera Sicinivirus, Anativirus, Megrivirus and Aalivirus. Most of these viruses were genetically different from other currently known viruses from the NCBI dataset. The study showed that the abundance and number of avian picornaviruses and parvoviruses varied considerably throughout the year, with the high number of virus reads in some of the duck samples highly suggestive of an active infection at the time of sampling. The detection and characterisation of several parvoviruses and picornaviruses from the individual duck samples also suggests co-infection, which may lead to the emergence of novel viruses through possible recombination. Therefore, as new and emerging diseases evolve, it is relevant to explore and monitor potential animal reservoirs in their natural habitat.
View Article and Find Full Text PDF

Download full-text PDF

Source
http://dx.doi.org/10.1038/s41598-020-69557-zDOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC7393117PMC
July 2020

No correlation between microbiota composition and blood parameters in nesting flatback turtles (Natator depressus).

Sci Rep 2020 05 20;10(1):8333. Epub 2020 May 20.

School of Biological Sciences, Monash University, Wellington Rd, Clayton, Victoria, 3800, Australia.

The microbiota is considered critical for normal vertebrate homeostasis and it may exert its effects at a local level within the gastrointestinal tract, or systemically through the production of bacterial metabolites. To date, investigations into the role that the microbiota plays in reptile physiology are rare. To address this knowledge gap, we explored the relationship between differences in microbial communities to see if they accounted for differences in haematology and biochemistry values, in different populations of nesting flatback turtles (Natator depressus). We found that microbiota composition was not correlated to any of the blood analytes we measured in flatbacks. This study is the first of its kind in reptiles and highlights the need for further investigations to determine mechanisms by which the microbiota influences the physiology and health of reptiles.
View Article and Find Full Text PDF

Download full-text PDF

Source
http://dx.doi.org/10.1038/s41598-020-65321-5DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC7239873PMC
May 2020

Long-term photo-id and satellite tracking reveal sex-biased survival linked to movements in an endangered species.

Ecology 2020 07 30;101(7):e03027. Epub 2020 Mar 30.

School of Life and Environmental Sciences, Deakin University, Geelong, Victoria, 3280, Australia.

Sex-biased survival linked to anthropogenic threats places populations at risk. We show the utility of long-term multidecadal photo-identification (photo-id) combined with long-term high-resolution (Fastloc-GPS) satellite telemetry to investigate the links between mortality rates and patterns of movement for a wide-ranging, endangered marine vertebrate. Using a photo-identification database of 947 loggerhead turtles (Caretta caretta) compiled over 18 yr, we estimated greater annual survival rates of females (0.89; 95% confidence interval [CI] 0.87-0.90) compared to males (0.73; 95% CI 0.67-0.78). For males satellite-tracked across multiple breeding seasons, 100% (26 of 26) returned to the same breeding site, suggesting the calculated lower male survival rate was likely not due to emigration to breed elsewhere. 10,111 and 2,524 tracking days for males (n = 39 individuals) and females (n = 18 individuals), respectively, revealed different habitat-use patterns outside the breeding season: males tended to occupy foraging sites closer to shore and closer to breeding sites but, due to their generally annual breeding, compared to biennial breeding for females, males migrated further per year on average. These differences in movement patterns likely contribute to higher mortality in males through increased interaction with anthropogenic threats. Long-term identification coupled with tracking offers great promise for estimating the survival rates of other wide-ranging species.
View Article and Find Full Text PDF

Download full-text PDF

Source
http://dx.doi.org/10.1002/ecy.3027DOI Listing
July 2020

Detection of a Reassortant H9N2 Avian Influenza Virus with Intercontinental Gene Segments in a Resident Australian Chestnut Teal.

Viruses 2020 01 13;12(1). Epub 2020 Jan 13.

Geelong Centre for Emerging Infectious Diseases, Geelong, Victoria 3220, Australia.

The present study reports the genetic characterization of a low-pathogenicity H9N2 avian influenza virus, initially from a pool and subsequently from individual faecal samples collected from Chestnut teals () in southeastern Australia. Phylogenetic analyses of six full gene segments and two partial gene segments obtained from next-generation sequencing showed that this avian influenza virus, A/Chestnut teal/Australia/CT08.18/12952/2018 (H9N2), was a typical, low-pathogenicity, Eurasian aquatic bird lineage H9N2 virus, albeit containing the North American lineage nucleoprotein (NP) gene segment detected previously in Australian wild birds. This is the first report of a H9N2 avian influenza virus in resident wild birds in Australia, and although not in itself a cause of concern, is a clear indication of spillover and likely reassortment of influenza viruses between migratory and resident birds, and an indication that any lineage could potentially be introduced in this way.
View Article and Find Full Text PDF

Download full-text PDF

Source
http://dx.doi.org/10.3390/v12010088DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC7019556PMC
January 2020

Serologic Evidence of Exposure to Highly Pathogenic Avian Influenza H5 Viruses in Migratory Shorebirds, Australia.

Emerg Infect Dis 2019 10;25(10):1903-1910

Highly pathogenic avian influenza (HPAI) H5Nx viruses of the goose/Guangdong/96 lineage continue to cause outbreaks in poultry and wild birds globally. Shorebirds, known reservoirs of avian influenza viruses, migrate from Siberia to Australia along the East-Asian-Australasian Flyway. We examined whether migrating shorebirds spending nonbreeding seasons in Australia were exposed to HPAI H5 viruses. We compared those findings with those for a resident duck species. We screened >1,500 blood samples for nucleoprotein antibodies and tested positive samples for specific antibodies against 7 HPAI H5 virus antigens and 2 low pathogenicity avian influenza H5 virus antigens. We demonstrated the presence of hemagglutinin inhibitory antibodies against HPAI H5 virus clade 2.3.4.4 in the red-necked stint (Calidris ruficolis). We did not find hemagglutinin inhibitory antibodies in resident Pacific black ducks (Anas superciliosa). Our study highlights the potential role of long-distance migratory shorebirds in intercontinental spread of HPAI H5 viruses.
View Article and Find Full Text PDF

Download full-text PDF

Source
http://dx.doi.org/10.3201/eid2510.190699DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC6759277PMC
October 2019

Virome heterogeneity and connectivity in waterfowl and shorebird communities.

ISME J 2019 10 25;13(10):2603-2616. Epub 2019 Jun 25.

Marie Bashir Institute for Infectious Diseases and Biosecurity, Charles Perkins Centre, School of Life and Environmental Sciences and Sydney Medical School, The University of Sydney, Sydney, Australia.

Models of host-microbe dynamics typically assume a single-host population infected by a single pathogen. In reality, many hosts form multi-species aggregations and may be infected with an assemblage of pathogens. We used a meta-transcriptomic approach to characterize the viromes of nine avian species in the Anseriformes (ducks) and Charadriiformes (shorebirds). This revealed the presence of 27 viral species, of which 24 were novel, including double-stranded RNA viruses (Picobirnaviridae and Reoviridae), single-stranded RNA viruses (Astroviridae, Caliciviridae, Picornaviridae), a retro-transcribing DNA virus (Hepadnaviridae), and a single-stranded DNA virus (Parvoviridae). These viruses comprise multi-host generalist viruses and those that are host-specific, indicative of both virome connectivity (host sharing) and heterogeneity (host specificity). Virome connectivity was apparent in two well described multi-host virus species -avian coronavirus and influenza A virus- and a novel Rotavirus species that were shared among some Anseriform species, while virome heterogeneity was reflected in the absence of viruses shared between Anseriformes and Charadriiformes, as well as differences in viral abundance and alpha diversity among species. Overall, we demonstrate complex virome structures across host species that co-exist in multi-species aggregations.
View Article and Find Full Text PDF

Download full-text PDF

Source
http://dx.doi.org/10.1038/s41396-019-0458-0DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC6775988PMC
October 2019

Corrigendum to "An experimental examination of interindividual variation in feather corticosterone content in the house sparrow, Passer domesticus in southeast Australia" [Gen. Comp. Endocrinol. 244 (2017) 93-100].

Gen Comp Endocrinol 2019 Sep 16;280:35. Epub 2019 Apr 16.

Centre for Integrative Ecology, School of Life and Environmental Sciences, Deakin University, Locked Bag 20000, Geelong, VIC 3220, Australia.

View Article and Find Full Text PDF

Download full-text PDF

Source
http://dx.doi.org/10.1016/j.ygcen.2019.04.007DOI Listing
September 2019

Meta-transcriptomics reveals a diverse antibiotic resistance gene pool in avian microbiomes.

BMC Biol 2019 04 8;17(1):31. Epub 2019 Apr 8.

Marie Bashir Institute for Infectious Diseases and Biosecurity and Sydney Medical School, The University of Sydney, Sydney, NSW, 2006, Australia.

Background: Antibiotic resistance is rendering common bacterial infections untreatable. Wildlife can incorporate and disperse antibiotic-resistant bacteria in the environment, such as water systems, which in turn serve as reservoirs of resistance genes for human pathogens. Anthropogenic activity may contribute to the spread of bacterial resistance cycling through natural environments, including through the release of human waste, as sewage treatment only partially removes antibiotic-resistant bacteria. However, empirical data supporting these effects are currently limited. Here we used bulk RNA-sequencing (meta-transcriptomics) to assess the diversity and expression levels of functionally viable resistance genes in the gut microbiome of birds with aquatic habits in diverse locations.

Results: We found antibiotic resistance genes in birds from all localities, from penguins in Antarctica to ducks in a wastewater treatment plant in Australia. Comparative analysis revealed that birds feeding at the wastewater treatment plant carried the greatest resistance gene burden, including genes typically associated with multidrug resistance plasmids as the aac(6)-Ib-cr gene. Differences in resistance gene burden also reflected aspects of bird ecology, taxonomy, and microbial function. Notably, ducks, which feed by dabbling, carried a higher abundance and diversity of resistance genes than turnstones, avocets, and penguins, which usually prey on more pristine waters.

Conclusions: These transcriptome data suggest that human waste, even if it undergoes treatment, might contribute to the spread of antibiotic resistance genes to the wild. Differences in microbiome functioning across different bird lineages may also play a role in the antibiotic resistance burden carried by wild birds. In summary, we reveal the complex factors explaining the distribution of resistance genes and their exchange routes between humans and wildlife, and show that meta-transcriptomics is a valuable tool to access functional resistance genes in whole microbial communities.
View Article and Find Full Text PDF

Download full-text PDF

Source
http://dx.doi.org/10.1186/s12915-019-0649-1DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC6454771PMC
April 2019

The adequacy of aging techniques in vertebrates for rapid estimation of population mortality rates from age distributions.

Ecol Evol 2019 Feb 27;9(3):1394-1402. Epub 2018 Dec 27.

Centre for Integrative Ecology, School of Life and Environmental Sciences Deakin University Geelong Victoria Australia.

As a key parameter in population dynamics, mortality rates are frequently estimated using mark-recapture data, which requires extensive, long-term data sets. As a potential rapid alternative, we can measure variables correlated to age, allowing the compilation of population age distributions, from which mortality rates can be derived. However, most studies employing such techniques have ignored their inherent inaccuracy and have thereby failed to provide reliable mortality estimates. In this study, we present a general statistical model linking birth rate, mortality rate, and population age distributions. We next assessed the reliability and data needs (i.e., sample size) for estimating mortality rate of eight different aging techniques. The results revealed that for half of the aging techniques, correlations with age varied considerably, translating into highly variable accuracies when used to estimate mortality rate from age distributions. Telomere length is generally not sufficiently correlated to age to provide reliable mortality rate estimates. DNA methylation, signal-joint T-cell recombination excision circle (sjTREC), and racemization are generally more promising techniques to ultimately estimate mortality rate, if a sufficiently high sample size is available. Otolith ring counts, otolithometry, and age-length keys in fish, and skeletochronology in reptiles, mammals, and amphibians, outperformed all other aging techniques and generated relatively accurate mortality rate estimation with a sample size that can be feasibly obtained. Provided the method chosen is minimizing and estimating the error in age estimation, it is possible to accurately estimate mortality rates from age distributions. The method therewith has the potential to estimate a critical, population dynamic parameter to inform conservation efforts within a limited time frame as opposed to mark-recapture analyses.
View Article and Find Full Text PDF

Download full-text PDF

Source
http://dx.doi.org/10.1002/ece3.4854DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC6374686PMC
February 2019

Extreme Competence: Keystone Hosts of Infections.

Trends Ecol Evol 2019 04 29;34(4):303-314. Epub 2019 Jan 29.

Environmental Futures Research Institute, Griffith University, Nathan, QLD 4111, Australia.

Individual hosts differ extensively in their competence for parasites, but traditional research has discounted this variation, partly because modeling such heterogeneity is difficult. This discounting has diminished as tools have improved and recognition has grown that some hosts, the extremely competent, can have exceptional impacts on disease dynamics. Most prominent among these hosts are the superspreaders, but other forms of extreme competence (EC) exist and others await discovery; each with potentially strong but distinct implications for disease emergence and spread. Here, we propose a framework for the study and discovery of EC, suitable for different host-parasite systems, which we hope enhances our understanding of how parasites circulate and evolve in host communities.
View Article and Find Full Text PDF

Download full-text PDF

Source
http://dx.doi.org/10.1016/j.tree.2018.12.009DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC7114649PMC
April 2019

A Divergent Hepatitis D-Like Agent in Birds.

Viruses 2018 12 17;10(12). Epub 2018 Dec 17.

WHO Collaborating Centre for Reference and Research on Influenza, The Peter Doherty Institute for Infection and Immunity, Melbourne, VIC 3000, Australia.

Hepatitis delta virus (HDV) is currently only found in humans and is a satellite virus that depends on hepatitis B virus (HBV) envelope proteins for assembly, release, and entry. Using meta-transcriptomics, we identified the genome of a novel HDV-like agent in ducks. Sequence analysis revealed secondary structures that were shared with HDV, including self-complementarity and ribozyme features. The predicted viral protein shares 32% amino acid similarity to the small delta antigen of HDV and comprises a divergent phylogenetic lineage. The discovery of an avian HDV-like agent has important implications for the understanding of the origins of HDV and sub-viral agents.
View Article and Find Full Text PDF

Download full-text PDF

Source
http://dx.doi.org/10.3390/v10120720DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC6315422PMC
December 2018

Virus-virus interactions and host ecology are associated with RNA virome structure in wild birds.

Mol Ecol 2018 12 22;27(24):5263-5278. Epub 2018 Nov 22.

Marie Bashir Institute for Infectious Diseases and Biosecurity, Charles Perkins Centre, School of Life and Environmental Sciences and Sydney Medical School, The University of Sydney, Sydney, New South Wales, Australia.

Little is known about the factors that shape the ecology of RNA viruses in nature. Wild birds are an important case in point, as other than influenza A virus, avian samples are rarely tested for viruses, especially in the absence of overt disease. Using bulk RNA-sequencing ("meta-transcriptomics"), we revealed the viral diversity present in Australian wild birds through the lens of the ecological factors that may determine virome structure and abundance. A meta-transcriptomic analysis of four Anseriformes (waterfowl) and Charadriiformes (shorebird) species sampled in temperate and arid Australia revealed the presence of 27 RNA virus genomes, 18 of which represent newly described species. The viruses identified included a previously described gammacoronavirus and influenza A viruses. Additionally, we identified novel virus species from the families Astroviridae, Caliciviridae, Reoviridae, Rhabdoviridae, Picobirnaviridae and Picornaviridae. We noted differences in virome structure that reflected underlying differences in location and influenza A infection status. Red-necked Avocets (Recurvirostra novaehollandiae) from Australia's arid interior possessed the greatest viral diversity and abundance, markedly higher than individuals sampled in temperate Australia. In Ruddy Turnstones (Arenaria interpres) and dabbling ducks (Anas spp.), viral abundance and diversity were higher and more similar in hosts that were positive for influenza A infection compared to those that were negative for this virus, despite samples being collected on the same day and from the same location. This study highlights the extent and diversity of RNA viruses in wild birds and lays the foundation for understanding the factors that determine virome structure in wild populations.
View Article and Find Full Text PDF

Download full-text PDF

Source
http://dx.doi.org/10.1111/mec.14918DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC6312746PMC
December 2018

The roles of migratory and resident birds in local avian influenza infection dynamics.

J Appl Ecol 2018 Nov 26;55(6):2963-2975. Epub 2018 Mar 26.

Deakin University, School of Life and Environmental Sciences, Centre for Integrative Ecology, Geelong, Australia.

Migratory birds are an increasing focus of interest when it comes to infection dynamics and the spread of avian influenza viruses (AIV). However, we lack detailed understanding migratory birds' contribution to local AIV prevalence levels and their downstream socio-economic costs and threats.To explain the potential differential roles of migratory and resident birds in local AIV infection dynamics, we used a susceptible-infectious-recovered (SIR) model. We investigated five (mutually non- exclusive) mechanisms potentially driving observed prevalence patterns: 1) a pronounced birth pulse (e.g. the synchronised annual influx of immunologically naïve individuals), 2) short-term immunity, 3) increase of susceptible migrants, 4) differential susceptibility to infection (i.e. transmission rate) for migrants and residents, and 5) replacement of migrants during peak migration.SIR models describing all possible combinations of the five mechanisms were fitted to individual AIV infection data from a detailed longitudinal surveillance study in the partially migratory mallard duck (). During autumn and winter, the local resident mallard community also held migratory mallards that exhibited distinct AIV infection dynamics.Replacement of migratory birds during peak migration in autumn was found to be the most important mechanism driving the variation in local AIV infection patterns. This suggests that a constant influx of migratory birds, likely immunological naïve to locally circulating AIV strains, is required to predict the observed temporal prevalence patterns and the distinct differences in prevalence between residents and migrants.. Our analysis reveals a key mechanism that could explain the amplifying role of migratory birds in local avian influenza virus infection dynamics; the constant flow and replacement of migratory birds during peak migration. Aside from monitoring efforts, in order to achieve adequate disease management and control in wildlife - with knock-on effects for livestock and humans, - we conclude that it is crucial, in future surveillance studies, to record host demographical parameters such as population density, timing of birth and turnover of migrants.
View Article and Find Full Text PDF

Download full-text PDF

Source
http://dx.doi.org/10.1111/1365-2664.13154DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC6188652PMC
November 2018

Turning natural adaptations to oncogenic factors into an ally in the war against cancer.

Evol Appl 2018 Jul 14;11(6):836-844. Epub 2018 Mar 14.

CREEC/MIVEGEC IRD CNRS University of Montpellier Montpellier France.

Both field and experimental evolution studies have demonstrated that organisms naturally or artificially exposed to environmental oncogenic factors can, sometimes rapidly, evolve specific adaptations to cope with pollutants and their adverse effects on fitness. Although numerous pollutants are mutagenic and carcinogenic, little attention has been given to exploring the extent to which adaptations displayed by organisms living in oncogenic environments could inspire novel cancer treatments, through mimicking the processes allowing these organisms to prevent or limit malignant progression. Building on a substantial knowledge base from the literature, we here present and discuss this progressive and promising research direction, advocating closer collaboration between the fields of medicine, ecology, and evolution in the war against cancer.
View Article and Find Full Text PDF

Download full-text PDF

Source
http://dx.doi.org/10.1111/eva.12608DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC5999213PMC
July 2018

Live bird markets in Bangladesh as a potentially important source for Avian Influenza Virus transmission.

Prev Vet Med 2018 Aug 2;156:22-27. Epub 2018 May 2.

Centre for Integrative Ecology, School of Life and Environmental Sciences, Deakin University, Geelong, VIC, Australia. Electronic address:

Live bird markets (LBM) are important for trading poultry in many developing countries where they are being considered hotspots of Avian Influenza Virus (AIV) prevalence and contamination. An active surveillance for Avian Influenza Virus (AIV) was conducted on four species of LBM birds (chickens, ducks, quails and pigeons) from 10 of the largest LBM in Chittagong, Bangladesh, and two species of peri-domestic wild birds (house crow and Asian pied starling) in their direct vicinity from November 2012 until September 2016. Our aim was to identify the scale and annual pattern of AIV circulation in both the LBM birds and the two per-domestic wild bird species living in close proximity of the LBM. In the latter two species, the annual pattern in AIV antibody prevalence was additionally investigated. A total of 4770 LBM birds and 1119 peri-domestic wild birds were sampled. We used rt-PCR for detection of the AIV M-gene and AIV subtypes H5, H7 and H9 from swab samples. We used c-ELISA for AIV antibody detection from serum samples of peri-domestic wild birds. Average AIV prevalence among the four LBM species varied between 16 and 28%, whereas no AIV was detected in peri-domestic wild birds by rt-PCR. In all LBM species we found significantly higher AIV prevalence in winter compared to summer. A similar pattern was found in AIV antibody prevalence in peri-domestic wild birds feeding in the direct vicinity of LBM. For the subtypes of AIV investigated, we found a significantly higher proportion of AIV H5 in LBM chickens and H9 in LBM ducks. No H7 was detected in any of the investigated samples. We conclude that AIV and notably AIV H5 and H9 were circulating in the investigated LBM of Bangladesh with clear seasonality that matched the prevalence of AIV antibodies of peri-domestic wild birds. These patterns show great resemblance to the annual outbreak patterns in Bangladeshi poultry industry. Our data suggest considerable exchange of AIV within and among the four LBM bird species and peri-domestic wild birds, which likely contributes to the maintenance of the AIV problems in Bangladesh. Increasing biosecurity and notably reducing the direct and indirect mixing of various domestic bird species and peri-domestic wild birds and developing all-in-all-out selling systems with regular use of disinfectant are likely to reduce the risk of transmission and spread of AIV, including HPAI.
View Article and Find Full Text PDF

Download full-text PDF

Source
http://dx.doi.org/10.1016/j.prevetmed.2018.05.003DOI Listing
August 2018

Metagenomics detection and characterisation of viruses in faecal samples from Australian wild birds.

Sci Rep 2018 06 6;8(1):8686. Epub 2018 Jun 6.

Geelong Centre for Emerging Infectious Diseases, Geelong, Victoria, 3220, Australia.

We present an optimised metagenomics method for detection and characterisation of all virus types including single and double stranded DNA/RNA and enveloped and non-enveloped viruses. Initial evaluation included both spiked and non-spiked bird faecal samples as well as non-spiked human faecal samples. From the non-spiked bird samples (Australian Muscovy duck and Pacific black ducks) we detected 21 viruses, and we also present a summary of a few viruses detected in human faecal samples. We then present a detailed analysis of selected virus sequences in the avian samples that were somewhat similar to known viruses, and had good quality (Q20 or higher) and quantity of next-generation sequencing reads, and was of interest from a virological point of view, for example, avian coronavirus and avian paramyxovirus 6. Some of these viruses were closely related to known viruses while others were more distantly related with 70% or less identity to currently known/sequenced viruses. Besides detecting viruses, the technique also allowed the characterisation of host mitochondrial DNA present and thus identifying host species, while ribosomal RNA sequences provided insight into the "ribosomal activity microbiome"; of gut parasites; and of food eaten such as plants or insects, which we correlated to non-avian host associated viruses.
View Article and Find Full Text PDF

Download full-text PDF

Source
http://dx.doi.org/10.1038/s41598-018-26851-1DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC5989203PMC
June 2018

Detection and characterisation of coronaviruses in migratory and non-migratory Australian wild birds.

Sci Rep 2018 04 13;8(1):5980. Epub 2018 Apr 13.

Geelong Centre for Emerging Infectious Diseases, Geelong, Victoria, Australia.

We evaluated the presence of coronaviruses by PCR in 918 Australian wild bird samples collected during 2016-17. Coronaviruses were detected in 141 samples (15.3%) from species of ducks, shorebirds and herons and from multiple sampling locations. Sequencing of selected positive samples found mainly gammacoronaviruses, but also some deltacoronaviruses. The detection rate of coronaviruses was improved by using multiple PCR assays, as no single assay could detect all coronavirus positive samples. Sequencing of the relatively conserved Orf1 PCR amplicons found that Australian duck gammacoronaviruses were similar to duck gammacoronaviruses around the world. Some sequenced shorebird gammacoronaviruses belonged to Charadriiformes lineages, but others were more closely related to duck gammacoronaviruses. Australian duck and heron deltacoronaviruses belonged to lineages with other duck and heron deltacoronaviruses, but were almost 20% different in nucleotide sequence to other deltacoronavirus sequences available. Deltacoronavirus sequences from shorebirds formed a lineage with a deltacoronavirus from a ruddy turnstone detected in the United States. Given that Australian duck gammacoronaviruses are highly similar to those found in other regions, and Australian ducks rarely come into contact with migratory Palearctic duck species, we hypothesise that migratory shorebirds are the important vector for moving wild bird coronaviruses into and out of Australia.
View Article and Find Full Text PDF

Download full-text PDF

Source
http://dx.doi.org/10.1038/s41598-018-24407-xDOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC5899083PMC
April 2018

Genetic diversity, inbreeding and cancer.

Proc Biol Sci 2018 03;285(1875)

Centre for Integrative Ecology, School of Life and Environmental Sciences, Deakin University, Waurn Ponds, Victoria 3216, Australia

Genetic diversity is essential for adaptive capacities, providing organisms with the potential of successfully responding to intrinsic and extrinsic challenges. Although a clear reciprocal link between genetic diversity and resistance to parasites and pathogens has been established across taxa, the impact of loss of genetic diversity by inbreeding on the emergence and progression of non-communicable diseases, such as cancer, has been overlooked. Here we provide an overview of such associations and show that low genetic diversity and inbreeding associate with an increased risk of cancer in both humans and animals. Cancer being a multifaceted disease, loss of genetic diversity can directly (via accumulation of oncogenic homozygous mutations) and indirectly (via increased susceptibility to oncogenic pathogens) impact abnormal cell emergence and escape of immune surveillance. The observed link between reduced genetic diversity and cancer in wildlife may further imperil the long-term survival of numerous endangered species, highlighting the need to consider the impact of cancer in conservation biology. Finally, the somewhat incongruent data originating from human studies suggest that the association between genetic diversity and cancer development is multifactorial and may be tumour specific. Further studies are therefore crucial in order to elucidate the underpinnings of the interactions between genetic diversity, inbreeding and cancer.
View Article and Find Full Text PDF

Download full-text PDF

Source
http://dx.doi.org/10.1098/rspb.2017.2589DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC5897632PMC
March 2018

Time versus energy minimization migration strategy varies with body size and season in long-distance migratory shorebirds.

Mov Ecol 2017 7;5:23. Epub 2017 Nov 7.

Centre for Integrative Ecology, School of Life and Environmental Sciences, Deakin University, Geelong, Australia.

Background: Migrants have been hypothesised to use different migration strategies between seasons: a time-minimization strategy during their pre-breeding migration towards the breeding grounds and an energy-minimization strategy during their post-breeding migration towards the wintering grounds. Besides season, we propose body size as a key factor in shaping migratory behaviour. Specifically, given that body size is expected to correlate negatively with maximum migration speed and that large birds tend to use more time to complete their annual life-history events (such as moult, breeding and migration), we hypothesise that large-sized species are time stressed all year round. Consequently, large birds are not only likely to adopt a time-minimization strategy during pre-breeding migration, but also during post-breeding migration, to guarantee a timely arrival at both the non-breeding (i.e. wintering) and breeding grounds.

Methods: We tested this idea using individual tracks across six long-distance migratory shorebird species (family Scolopacidae) along the East Asian-Australasian Flyway varying in size from 50 g to 750 g lean body mass. Migration performance was compared between pre- and post-breeding migration using four quantifiable migratory behaviours that serve to distinguish between a time- and energy-minimization strategy, including migration speed, number of staging sites, total migration distance and step length from one site to the next.

Results: During pre- and post-breeding migration, the shorebirds generally covered similar distances, but they tended to migrate faster, used fewer staging sites, and tended to use longer step lengths during pre-breeding migration. These seasonal differences are consistent with the prediction that a time-minimization strategy is used during pre-breeding migration, whereas an energy-minimization strategy is used during post-breeding migration. However, there was also a tendency for the seasonal difference in migration speed to progressively disappear with an increase in body size, supporting our hypothesis that larger species tend to use time-minimization strategies during both pre- and post-breeding migration.

Conclusions: Our study highlights that body size plays an important role in shaping migratory behaviour. Larger migratory bird species are potentially time constrained during not only the pre- but also the post-breeding migration. Conservation of their habitats during both seasons may thus be crucial for averting further population declines.
View Article and Find Full Text PDF

Download full-text PDF

Source
http://dx.doi.org/10.1186/s40462-017-0114-0DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC5674797PMC
November 2017

Active migration is associated with specific and consistent changes to gut microbiota in Calidris shorebirds.

J Anim Ecol 2018 03 18;87(2):428-437. Epub 2017 Dec 18.

Centre for Integrative Ecology, Deakin University, Geelong, Vic., Australia.

Gut microbes are increasingly recognised for their role in regulating an animal's metabolism and immunity. However, identifying repeatable associations between host physiological processes and their gut microbiota has proved challenging, in part because microbial communities often respond stochastically to host physiological stress (e.g. fasting, forced exercise or infection). Migratory birds provide a valuable system in which to test host-microbe interactions under physiological extremes because these hosts are adapted to predictable metabolic and immunological challenges as they undergo seasonal migrations, including temporary gut atrophy during long-distance flights. These physiological challenges may either temporarily disrupt gut microbial ecosystems, or, alternatively, promote predictable host-microbe associations during migration. To determine the relationship between migration and gut microbiota, we compared gut microbiota composition between migrating and non-migrating ("resident") conspecific shorebirds sharing a flock. We performed this across two sandpiper species, Calidris ferruginea and Calidris ruficollis, in north-western Australia, and an additional C. ruficollis population 3,000 km away in southern Australia. We found that migrants consistently had higher abundances of the bacterial genus Corynebacterium (average 28% abundance) compared to conspecific residents (average <1% abundance), with this effect holding across both species and sites. However, other than this specific association, community structure and diversity was almost identical between migrants and residents, with migration status accounting for only 1% of gut community variation when excluding Corynebacterium. Our findings suggest a consistent relationship between Corynebacterium and Calidris shorebirds during migration, with further research required to identify causal mechanisms behind the association, and to elucidate functionality to the host. However, outside this specific association, migrating shorebirds broadly maintained gut community structure, which may allow them to quickly recover gut function after a migratory flight. This study provides a rare example of a repeatable and specific response of the gut microbiota to a major physiological challenge across two species and two distant populations.
View Article and Find Full Text PDF

Download full-text PDF

Source
http://dx.doi.org/10.1111/1365-2656.12784DOI Listing
March 2018

Migratory animals feel the cost of getting sick: A meta-analysis across species.

J Anim Ecol 2018 Jan 20;87(1):301-314. Epub 2017 Nov 20.

Centre for Integrative Ecology, Deakin University, Geelong, Vic., Australia.

Migratory animals are widely assumed to play an important role in the long-distance dispersal of parasites, and are frequently implicated in the global spread of zoonotic pathogens such as avian influenzas in birds and Ebola viruses in bats. However, infection imposes physiological and behavioural constraints on hosts that may act to curtail parasite dispersal via changes to migratory timing ("migratory separation") and survival ("migratory culling"). There remains little consensus regarding the frequency and extent to which migratory separation and migratory culling may operate, despite a growing recognition of the importance of these mechanisms in regulating transmission dynamics in migratory animals. We quantitatively reviewed 85 observations extracted from 41 studies to examine how both infection status and infection intensity are related to changes in body stores, refuelling rates, movement capacity, phenology and survival in migratory hosts across taxa. Overall, host infection status was weakly associated with reduced body stores, delayed migration and lower survival, and more strongly associated with reduced movement. Infection intensity was not associated with changes to host body stores, but was associated with moderate negative effects on movement, phenology and survival. In conclusion, we found evidence for negative effects of infection on host phenology and survival, but the effects were relatively small. This may have implications for the extent to which migratory separation and migratory culling act to limit parasite dispersal in migratory systems. We propose a number of recommendations for future research that will further advance our understanding of how migratory separation and migratory culling may shape host-parasite dynamics along migratory routes globally.
View Article and Find Full Text PDF

Download full-text PDF

Source
http://dx.doi.org/10.1111/1365-2656.12766DOI Listing
January 2018

Seasonal reproductive tactics: annual timing and the capital-to-income breeder continuum.

Philos Trans R Soc Lond B Biol Sci 2017 Nov;372(1734)

Research Institute of Wildlife Ecology, University of Veterinary Medicine Vienna, 1160 Vienna, Austria.

Tactics of resource use for reproduction are an important feature of life-history strategies. A distinction is made between 'capital' breeders, which finance reproduction using stored energy, and 'income' breeders, which pay for reproduction using concurrent energy intake. In reality, vertebrates use a continuum of capital-to-income tactics, and, for many species, the allocation of capital towards reproduction is a plastic trait. Here, we review how trophic interactions and the timing of life-history events are influenced by tactics of resource use in birds and mammals. We first examine how plasticity in the allocation of capital towards reproduction is linked to phenological flexibility via interactions between endocrine/neuroendocrine control systems and the sensory circuits that detect changes in endogenous state, and environmental cues. We then describe the ecological drivers of reproductive timing in species that vary in the degree to which they finance reproduction using capital. Capital can be used either as a mechanism to facilitate temporal synchrony between energy supply and demand or as a means of lessening the need for synchrony. Within many species, an individual's ability to cope with environmental change may be more tightly linked to plasticity in resource allocation than to absolute position on the capital-to-income breeder continuum.This article is part of the themed issue 'Wild clocks: integrating chronobiology and ecology to understand timekeeping in free-living animals'.
View Article and Find Full Text PDF

Download full-text PDF

Source
http://dx.doi.org/10.1098/rstb.2016.0250DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC5647277PMC
November 2017

Gut microbiota of a long-distance migrant demonstrates resistance against environmental microbe incursions.

Mol Ecol 2017 Oct 28;26(20):5842-5854. Epub 2017 Sep 28.

Centre for Integrative Ecology, Deakin University, Geelong, Vic., Australia.

Migratory animals encounter suites of novel microbes as they move between disparate sites during their migrations, and are frequently implicated in the global spread of pathogens. Although wild animals have been shown to source a proportion of their gut microbiota from their environment, the susceptibility of migrants to enteric infections may be dependent upon the capacity of their gut microbiota to resist incorporating encountered microbes. To evaluate migrants' susceptibility to microbial invasion, we determined the extent of microbial sourcing from the foraging environment and examined how this influenced gut microbiota dynamics over time and space in a migratory shorebird, the Red-necked stint Calidris ruficollis. Contrary to previous studies on wild, nonmigratory hosts, we found that stint on their nonbreeding grounds obtained very little of their microbiota from their environment, with most individuals sourcing only 0.1% of gut microbes from foraging sediment. This microbial resistance was reflected at the population level by only weak compositional differences between stint flocks occupying ecologically distinct sites, and by our finding that stint that had recently migrated 10,000 km did not differ in diversity or taxonomy from those that had inhabited the same site for a full year. However, recent migrants had much greater abundances of the genus Corynebacterium, suggesting a potential microbial response to either migration or exposure to a novel environment. We conclude that the gut microbiota of stint is largely resistant to invasion from ingested microbes and that this may have implications for their susceptibility to enteric infections during migration.
View Article and Find Full Text PDF

Download full-text PDF

Source
http://dx.doi.org/10.1111/mec.14326DOI Listing
October 2017

Are Poultry or Wild Birds the Main Reservoirs for Avian Influenza in Bangladesh?

Ecohealth 2017 09 15;14(3):490-500. Epub 2017 Jun 15.

Centre for Integrative Ecology, School of Life and Environmental Sciences, Deakin University, Geelong, Australia.

Avian influenza viruses (AIV) are of great socioeconomic and health concern, notably in Southeast Asia where highly pathogenic strains, such as highly pathogenic avian influenza (HPAI) H5N1 and other H5 and H7 AIVs, continue to occur. Wild bird migrants are often implicated in the maintenance and spread of AIV. However, little systematic surveillance of wild birds has been conducted in Southeast Asia to evaluate whether the prevalence of AIV in wild birds is higher than in other parts of the world where HPAI outbreaks occur less frequently. Across Bangladesh, we randomly sampled a total of 3585 wild and domestic birds to assess the prevalence of AIV and antibodies against AIV and compared these with prevalence levels found in other endemic and non-endemic countries. Our study showed that both resident and migratory wild birds in Bangladesh do not have a particularly elevated AIV prevalence and AIV sero-prevalence compared to wild birds from regions in the world where H5N1 is not endemic and fewer AIV outbreaks in poultry occur. Like elsewhere, notably wild birds of the orders Anseriformes were identified as the main wild bird reservoir, although we found exceptionally high sero-prevalence in one representative of the order Passeriformes, the house crow (Corvus splendens), importantly living on offal from live bird markets. This finding, together with high sero- and viral prevalence levels of AIV in domestic birds, suggests that wild birds are not at the base of the perpetuation of AIV problems in the local poultry sector, but may easily become victim to AIV spill back from poultry into some species of wild birds, potentially assisting in further spread of the virus.
View Article and Find Full Text PDF

Download full-text PDF

Source
http://dx.doi.org/10.1007/s10393-017-1257-6DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC5662684PMC
September 2017

Purifying selection and concerted evolution of RNA-sensing toll-like receptors in migratory waders.

Infect Genet Evol 2017 09 18;53:135-145. Epub 2017 May 18.

Centre for Integrative Ecology, School of Life and Environmental Sciences, Deakin University, Waurn Ponds, VIC 3216, Australia. Electronic address:

Migratory birds encounter a broad range of pathogens during their journeys, making them ideal models for studying immune gene evolution. Despite the potential value of these species to immunoecology and disease epidemiology, previous studies have typically focused on their adaptive immune gene repertoires. In this study, we examined the evolution of innate immune genes in three long-distance migratory waders (order Charadriiformes). We analysed two parts of the extracellular domains of two Toll-like receptors (TLR3 and TLR7) involved in virus recognition in the Sanderling (Calidris alba), Red-necked Stint (Calidris ruficollis), and Ruddy Turnstone (Arenaria interpres). Our analysis was extended to 50 avian species for which whole-genome sequences were available, including two additional waders. We found that the inferred relationships among avian TLR3 and TLR7 do not match the whole-genome phylogeny of birds. Further analyses showed that although both loci are predominantly under purifying selection, the evolution of the extracellular domain of avian TLR3 has also been driven by episodic diversifying selection. TLR7 was found to be duplicated in all five wader species and in two other orders of birds, Cuculiformes and Passeriformes. The duplication is likely to have occurred in the ancestor of each order, and the duplicated copies appear to be undergoing concerted evolution. The phylogenetic relationships of wader TLR7 matched those of the five wader species, but that of TLR3 did not. Instead, the tree inferred from TLR3 showed potential associations with the species' ecology, including migratory behaviour and exposure to pathogens. Our study demonstrates the importance of combining immunological and ecological knowledge to understand the impact of immune gene polymorphism on the evolutionary ecology of infectious diseases.
View Article and Find Full Text PDF

Download full-text PDF

Source
http://dx.doi.org/10.1016/j.meegid.2017.05.012DOI Listing
September 2017