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Klaassen, M.

Publications and source records attributed to Klaassen, M..

At least 19 recordsLinked to original sources

Integrating dedicated and opportunistic surveys to estimate seasonal common dolphin density off mainland Portugal

1. Common dolphins (Delphinus delphis) are the most abundant cetaceans off mainland Portugal and a species of conservation and bycatch concern, so reliable abundance estimates are a management priority. Yet no single survey provides adequate spatiotemporal coverage: dedicated programmes offer sparse snapshots, while opportunistic programmes are spatially constrained by their routes. Integrating them is methodologically demanding, and the existing methods that do so in a single model estimate the density of animal groups, not of the individual animals that management often requires. 2. We develop a spatiotemporal marked log-Gaussian Cox process that integrates four structurally distinct surveys through a shared intensity surface, comprising environmental covariates, a latent spatial field, and survey-specific detection functions. Group size enters as a zero-truncated negative binomial mark with its own spatiotemporal field. We apply it to a dedicated aerial survey and three opportunistic ship-based programmes off mainland Portugal, comprising 162,514 km of on-effort transects and 1,756 sightings of 17,000 animals. We fit the model in a Bayesian framework with integrated nested Laplace approximations, yielding seasonally resolved group and animal density surfaces across the Portuguese Exclusive Economic Zone, and abundance estimates with fully propagated uncertainty. 3. Predicted animal density concentrated over the shelf and upper slope in every season, peaking northwest, and increased in shallower, cooler, more productive waters and over steeper seabed. Abundance nearly doubled from summer (77,000 [95% credible interval: 60,000, 98,000]) to winter (146,000 [99,000, 208,000]). Seasons shared 56% of the spatial field's variance, so effort from any programme in any season informed all others, and the seasonal contrast remained estimable despite uneven coverage. 4. Synthesis and applications. Our framework allows managers to combine dedicated surveys with existing platforms of opportunity to estimate animal density by season. Because group size is modelled explicitly, densities are estimated in animals rather than groups, as required for bycatch risk assessment and marine spatial planning. Because each survey enters through its own observation model, the approach accommodates programmes that differ in platform and protocol and transfers to any species or region where several surveys each cover part of a population.

ecology↗

Migratory bird and marine mammal surveillance fails to find evidence for an HPAI H5N1 2.3.4.4b incursion into Australia in 2025

The panzootic caused by high pathogenicity avian influenza (HPAI) H5N1 clade 2.3.4.4b has been devastating for animals, globally. Despite global spread, the virus remains absent in Oceania. Herein we report the results of our fourth year of enhanced migratory bird surveillance, coinciding with the spring migration of wild birds in 2025; none of the 847 migratory wild birds or 38 marine mammals were positive for HPAI H5N1, although we did detect LPAI. Surveillance remains a critical tool for HPAI H5N1 response, with early detection and rapid response being critical to mitigate the impacts of this virus on animal, environment and human health.

microbiology↗

Ecological predictability emerges at the population level in phytoplankton communities

Predicting the composition and dynamics of ecological communities is challenging because complexity increases rapidly with species richness. A common strategy is to adopt a reductionist framework in which community dynamics are inferred from simpler components, such as population-level parameters or organismal traits. However, it remains unclear at which level of biological organization ecological predictability emerges. Here we experimentally test this reductionist cascade in marine phytoplankton communities. We first ask whether multispecies dynamics can be quantitatively predicted from demographic parameters measured in monocultures and species pairs. We then test whether these predictive parameters can themselves be inferred from organismal traits, focusing on cell size. We find that community composition is highly reproducible and can be accurately predicted from population-level parameters measured in simpler experimental settings. In contrast, these parameters do not show systematic relationships with cell size and cannot be predicted from this commonly used trait. These results demonstrate that ecological predictability emerges at the population level, where demographic parameters capture the combined effects of underlying biological processes, but resist further reduction to simple trait-based descriptions, suggesting that ecological interactions reshape organismal performance across levels of organisation.

ecology↗

Ecology of low pathogenicity avian influenza virus H7 in wild birds in south-eastern Australia prior to emergence of high pathogenicity avian influenza H7 in poultry

Adding to the global burden of high pathogenicity avian influenza (HPAI) H5N1, an unprecedented five HPAI H7 outbreaks occurred globally in 2024. Of these, three occurred in southeast Australia, with the independent emergence of HPAI H7N9, H7N8, and H7N3, resulting in the destruction of 2 million poultry. Historical data demonstrates that H7 outbreaks in Australia do not occur randomly, rather, there is a strong association between the timing of the previous H7 outbreaks and rainfall patterns in southeastern Australia. We aimed to address a hypothesis wherein prior to H7 outbreaks in poultry, there was a detectable change in H7 prevalence and/or virus diversity in wild bird populations. We addressed this using virological and serological surveillance data generated from multiple programs. Despite the collection of thousands of samples, there was only weak evidence to support our hypothesis, which provides strong incentive to evaluate current surveillance approaches for the purposes of risk prediction. However, in alignment with a previous analysis, there is strong support for a relationship between H7 outbreak probability and rainfall patterns across southeast Australia. Overall, improved understanding of the ecology and evolution of H5 and H7 viruses in wild bird reservoirs is pivotal to global disease preparedness and response.

microbiology↗

Spatiotemporal data integration for marine megafauna SDMs in dynamic environments: A point process approach

Species distribution models (SDMs) are widely used to predict where and when species occur, but the data available to fit them often resolve space and time unevenly. Designed surveys, such as line-transect distance-sampling surveys, provide structured spatial coverage and the detection information needed to estimate detectability, but logistical and funding constraints often limit them to short, infrequent periods. Opportunistic or citizen-science records are collected more frequently across the year, but from areas shaped by observer access and interest rather than survey design, and usually without comparable detection information. As a result, models built from either source alone tend to capture spatial structure or temporal dynamics well, but not both, limiting predictions for mobile species in dynamic environments. Here, we present a general framework, based on a log-Gaussian Cox process (LGCP) fitted using integrated nested Laplace approximations (INLA), that links multiple data sources to a shared spatiotemporal measure of species density through source-specific observation models: a detection function for survey transects, and spatial constraints reflecting the footprint of opportunistic effort. We apply the framework to cetacean line-transect surveys and whale-watching records. In a simulation with one month of survey data and twelve months of opportunistic data, the integrated model recovered spatiotemporal distribution patterns well (median correlation with the true pattern = 0.91) and estimated monthly abundance with a mean error of +10.7%, outperforming single-source models. In a case study of common dolphins (Delphinus delphis) off mainland Portugal, integration improved the spatial accuracy of predictions, although weak covariate effects limited the temporal variation the model could resolve. These results show that integration adds the most value when the two data sources resolve complementary aspects of distribution, in this case broad spatial structure from the survey and temporal replication from whale-watching, while temporal predictions remain limited when covariates carry weak seasonal signal. The framework is general and can be extended to other taxa, systems, and combinations of structured and opportunistic data by substituting the relevant observation models.

ecology↗

Surveillance of migratory shorebirds and seabirds in 2024 in Australia reveals incursions of a diversity of low pathogenicity avian influenza viruses, but not high pathogenicity avian influenza H5N1

The current panzootic of high pathogenicity avian influenza (HPAI) H5N1 has been catastrophic for wildlife, and following a significant sweep, clade 2.3.4.4b is found in every region aside from Oceania. Herein, we report the results of our third year of targeted surveillance of incoming migratory seabirds and shorebirds into Australia. We did not find evidence of HPAI H5N1 in any of the birds tested, and there were no reports of HPAI H5N1 in wildlife tested through other surveillance schemes in 2024. Unlike previous years, we detected a diversity of low pathogenicity avian influenza (LPAI) viruses in shorebirds. Through phylogenetic analysis we revealed that the H3N7 and H4N7 viruses recovered from Red-necked Stints were complex mosaic viruses, comprising segments of Eurasian, Australian shorebird, and Australian waterfowl segments. A H1N7 virus detected comprised a wholly Eurasian introduction, confirming this route for avian influenza viruses into Australian ecosystems. These results provide further evidence for the key role of long-distance migratory shorebirds in introducing novel LPAI viruses into Oceania. While our focus on northern migration routes remained appropriate for HPAI H5N1 surveillance in 2024, the continued spread of HPAI H5N1 to sub-Antarctic Islands demands consideration of a potential southern incursion route for Oceania in future.

microbiology↗

Contrasting dynamics of two incursions of low pathogenicity avian influenza virus into Australia

The current panzootic of high pathogenicity avian influenza virus H5N1 demonstrates how viral incursions can have major ramifications for wildlife and domestic animals. Herein, we describe the recent incursion into Australia of two low pathogenicity avian influenza virus subtypes, H4 and H10, that exhibited contrasting evolutionary dynamics. Viruses detected from national surveillance and disease investigations between 2020-2022 revealed 27 genomes, 24 of which have at least one segment more closely related to Eurasian or North American avian influenza lineages than those already circulating in Australia. Phylogenetic analysis revealed that H4 viruses circulating in shorebirds represent a recent incursion from Asia that is distinct from those circulating concurrently in Australian waterfowl. Analysis of the internal segments further demonstrates exclusive, persistent circulation in shorebirds. This contrasts with H10, where a novel lineage has emerged in wild waterfowl, poultry and captive birds across Australia, and has likely replaced previously circulating H10 lineages through competitive exclusion. Elucidating different dynamics for avian influenza incursions supports effective disease risk identification and communication that better informs disease preparedness and response.

microbiology↗

Long distance avian migrants fail to bring 2.3.4.4b HPAI H5N1 into Australia for a second year in a row

There is an ongoing and profound burden of lineage 2.3.4.4b high pathogenicity avian influenza (HPAI) H5N1 on wildlife and poultry, globally. Herein we report the continued absence of HPAI and antibodies against lineage 2.3.4.4b HPAI from October - December 2023, in migratory birds shortly after their arrival in Australia. Given the ever-changing phenotype of this virus, worldwide studies on the occurrence, or here absence of the virus, are of critical importance to understand the virus dispersal and incursion risk and development of response strategies.

microbiology↗

Fending for oneself or partnering up: Competition between mixo- and heterotrophic ciliates under dynamic resource supply

The outcome of species competition strongly depends on the traits of the competitors and associated trade-offs, as well as on environmental variability. Here we investigate the relevance of consumer trait variation for species coexistence in a ciliate consumer - microalgal prey system under fluctuating regimes of resource supply. We focus on consumer competition and feeding traits, and specifically on the consumers ability to overcome periods of resource limitation by mixotrophy, i.e. the ability of photosynthetic carbon fixation via algal symbionts in addition to phagotrophy. In a 48-day chemostat experiment, we investigated competitive interactions of different heterotrophic and mixotrophic ciliates of the genera Euplotes and Coleps under different resource regimes, providing prey either continuously or in pulses under constant or fluctuating light, entailing periods of resource depletion in fluctuating environments, but overall providing the same amount of prey and light. Although ultimate competition results remained unaffected, population dynamics of mixotrophic and heterotrophic ciliates were significantly altered by resource supply mode. However, the effects differed among species combinations and changed over time. Whether mixotrophs or heterotrophs dominated in competition strongly depended on the genera of the competing species and thus species-specific differences in the minimum resource requirements that are associated with feeding on shared prey, nutrient uptake, light harvesting and access to additional resources such as bacteria. Potential differences in the curvature of the species resource-dependent growth functions may have further mediated the species-specific responses to the different resource supply modes. In addition, while the presence of a heterotrophic competitor may have a direct negative effect on the growth rate of a mixotrophic species through grazing on a shared prey species, its presence may also have an indirect positive effect on the growth rate of the mixotroph by reducing competition between the autotroph and mixotroph for shared nutrients and light. Our study thus demonstrates that complex trophic interactions determine the outcome of competition, which can only be understood by taking on a multidimensional trait perspective.

ecology↗

Pervasive morphological responses to climate change in bird body and appendage size

Changes to body size and shape have been identified as potential adaptive responses to climate change, but the pervasiveness of these responses is questioned. To address this, we measured body and appendage size from 5013 museum bird skins of ecologically and evolutionary diverse species. We found that morphological change is a shared response to climate change across birds. Birds increased bill surface area, tarsus length, and relative wing length through time, consistent with expectations of increasing appendage size in warmer climates. Furthermore, birds decreased in absolute wing length, consistent with the expectation of decreasing body size in warmer climates. Interestingly, these trends were generally consistent across different diets, foraging habitats, and migratory and thermoregulatory behaviours. Shorter-term responses to hot weather were contrary to long-term effects for appendages. Overall, our findings support that morphological adaptation is a widespread response to climate change in birds that is independent of other ecological traits.

evolutionary biology↗

Wild birds' plight and role in the current bird flu panzootic

The current avian influenza panzootic is unprecedented and catastrophic for birds. With a focus on the implications of this panzootic for poultry, there is limited attention on wild birds. We highlight shortcomings and geographic biases in reporting leading to a severe underappreciation of wildlife mortality. We estimate the scale of mortality amongst wild birds is in the millions rather than tens-of-thousands reported, through comparison of notification data to accounts literature. The outbreaks amongst wild birds are causing population and species level concerns which may drive extinctions and jeopardise decades of conservation efforts.

microbiology↗

Interplay between pollution and avian influenza virus infection risk in shorebirds and waterfowl

Anthropogenic pollution may disrupt wildlife immune function and increase susceptibility to, and ability to withstand, infection. Of particular concern is avian influenza virus (AIV), which in its low-pathogenic form is endemic in many wild bird populations, notably waterfowl and shorebirds, and in its high-pathogenic form poses a threat to wildlife, livestock and people. Many pollutants have immunomodulative properties, yet little is known about how these pollutants affect AIV infection risk specifically. We examined concentrations of known immunomodulatory compounds, per- and polyfluoroalkyl substances (PFASs), and assessed their influence on AIV infection in three reservoir species, red-necked stint (Calidris ruficollis, n=121), pacific black duck (Anas superciliosa, n=57) and grey teal (Anas gracilis, n= 62). Using data on viral prevalence (cloacal/oropharyngeal swabs) and seroprevalence (AIV anti-nucleoprotein antibodies), we found no significant effect of PFASs pollution (total PFASs <0.01 - 470 ng/g in red-necked stint, <0.01 - 600 ng/g in pacific black duck and 0.3 - 200 ng/g in grey teal) on infection status in our three species. This may be due to relatively low pollutant concentrations, but we cannot rule out possible population culling through a synergy of pollution and infection stressors. We therefore recommend further studies on infection incidence in more polluted populations or species.

ecology↗

Assessment of contaminants, health and survival of migratory shorebirds in natural versus artificial wetlands - the potential of wastewater treatment plants as alternative habitats

The rapid destruction of natural wetland habitats over past decades has been partially offset by an increase in artificial wetlands. However, these also include wastewater treatment plants, which may pose a pollution risk to the wildlife using them. We studied two long-distance Arctic-breeding migratory shorebird species, curlew sandpiper (Calidris ferruginea, n=70) and red-necked stint (Calidris ruficollis, n=100), while on their Australian non-breeding grounds using a natural wetland versus an artificial wetland at a wastewater treatment plant (WTP). We compared pollutant exposure (elements and per- and poly-fluoroalkyl substances/PFASs), disease (avian influenza), physiological status (oxidative stress) of the birds at the two locations from 2011-2020, and population survival from 1978-2019. Our results indicated no significant differences in blood pellet pollutant concentrations between the habitats except mercury (WTP median: 224 ng/g, range: 19-873 ng/g; natural wetland: 160 ng/g, 22-998 ng/g) and perfluorooctanesulfonic acid (WTP median: 52 ng/g, range: <0.01-1280 ng/g; natural wetland: 14 ng/g, <0.01-379 ng/g) which were higher at the WTP, and selenium which was lower at the WTP (WTP median: 5000 ng/g, range: 1950-34400 ng/g; natural wetland: 19200 ng/g, 4130-65200 ng/g). We also measured higher blood o,o-dityrosine (an indicator of protein damage) at the WTP. No significant differences were found for adult survival, but survival of immature birds at the WTP appeared to be lower which could be due to higher dispersal to other wetlands. Interestingly, we found active avian influenza infections were higher in the natural habitat, while seropositivity was higher in the WTP, seemingly not directly related to pollutant exposure. Overall, we found negligible differences in pollutant exposure, health and survival of the shorebirds in the two habitats. Our findings suggest that appropriately managed wastewater treatment wetlands may provide a suitable alternative habitat to these migratory species, curbing the decline of shorebird populations from widespread habitat loss.

ecology↗

No evidence for HPAI H5N1 2.3.4.4b incursion into Australia in 2022

There is an ongoing and profound burden of lineage 2.3.4.4b high pathogenicity avian influenza (HPAI) H5 on wild birds and poultry, globally. Herein we report the continued absence of HPAI in Australia from September - December 2022, in inbound migratory birds. Given the ever changing phenotype of this virus, worldwide studies on the occurence, or here absence of the virus, are of critical importance to understand the virus dispersal and incursion risk and development of response strategies.

microbiology↗

Strong phylogenetic and ecological effects on host competency for avian influenza in Australian wild birds

Host susceptibility to parasites is mediated by intrinsic and external factors such as genetics, age or season. While key features have been revealed for avian influenza A virus (AIV) in waterfowl of the Northern Hemisphere, the role of host phylogeny has received limited attention. Herein, we analysed 12339 oropharyngeal and cloacal swabs and 10826 serum samples collected over 11 years from wild birds in Australia. As well as describing species-level differences in prevalence and seroprevalence, we reveal that host phylogeny is a key driver in susceptibility. We confirm the role of age in AIV seroprevalence and viral prevalence. Seasonality effects appear less pronounced than in the Northern Hemisphere, while annual variations are potentially linked to El Nino- Southern Oscillation. Taken together, our study provides new insights into evolutionary ecology of AIV in its avian hosts, defining distinctive processes on the continent of Australia and expanding our understanding of AIV globally.

microbiology↗

Australia as a global sink for the genetic diversity of avian influenza A virus

Most of our understanding of the ecology and evolution of avian influenza A virus (AIV) in wild birds is derived from studies conducted in the northern hemisphere on waterfowl, with a substantial bias towards dabbling ducks. However, relevant environmental conditions and patterns of avian migration and reproduction are substantially different in the southern hemisphere. Through the sequencing and analysis of 333 unique AIV genomes collected from wild birds collected over 15 years we show that Australia is a global sink for AIV diversity and not integrally linked with the Eurasian gene pool. Rather, AIV are infrequently introduced to Australia, followed by decades of isolated circulation and eventual extinction. The number of co-circulating viral lineages varies per subtype. AIV haemagglutinin (HA) subtypes that are rarely identified at duck-centric study sites (H8-12) had more detected introductions and contemporary co-circulating lineages in Australia. Combined with a lack of duck migration beyond the Australian-Papuan region, these findings suggest introductions by long-distance migratory shorebirds. In addition, we found no evidence of directional or consistent patterns in virus movement across the Australian continent. This feature corresponds to patterns of bird movement, whereby waterfowl have nomadic and erratic rainfall-dependant distributions rather than consistent intra-continental migratory routes. Finally, we detected high levels of virus gene segment reassortment, with a high diversity of AIV genome constellations across years and locations. These data, in addition to those from other studies in Africa and South America, clearly show that patterns of AIV dynamics in the Southern Hemisphere are distinct from those in the temperate north. Author SummaryA result of the ever-growing poultry industry is a dramatic global increase in the incidence of high pathogenicity avian influenza virus outbreaks. In contrast, wild birds are believed to be the main reservoir for low pathogenic avian influenza A virus. Due to intensive research and surveillance of AIV in waterfowl in the Northern Hemisphere, we have a better understanding of AIV ecology and evolution in that region compared to the Southern Hemisphere, which are characterised by different patterns of avian migration and ecological conditions. We analysed 333 unique AIV genomes collected from wild birds in Australia to understand how Australia fits into global AIV dynamics and how viruses are maintained and dispersed within the continent of Australia. We show that the Southern Hemisphere experiences differing evolutionary dynamics to those seen in Northern Hemisphere with Australia representing a global sink for AIV.

evolutionary biology↗

Host age shapes virome abundance and diversity in birds

Host age influences the ecology of many microorganisms. This is evident in one-host - one virus systems, such as influenza A virus in Mallards, but also in community studies of parasites and microbiomes. We used a meta-transcriptomic approach to assess whether host age is associated with differences in the abundance and diversity of avian viromes. We used samples from cohabiting Ruddy Turnstones (Arenaria interpres) across three age groups, collected at two contrasting points in their annual migratory cycle. Overall, we identified 14 viruses that likely infect birds, 11 of which were novel, including members of the Reoviridae, Astroviridae, Picornaviridae, and Phenuiviridae. Strikingly, 12 of the viruses identified were from juvenile birds sampled in the first year of their life, compared to only two viruses in adult birds. Similarly, both viral abundance and alpha diversity were higher in juvenile than adult birds. Notably, time of sampling had no association with virome structure such that the migratory period may not play a major role in structuring avian viromes. As well as informing studies of virus ecology, that host age impacts viral assemblages is a critical consideration for the future surveillance of novel and emerging viruses.

microbiology↗

Virome heterogeneity and connectivity in waterfowl and shorebird communities

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 and heterogeneity. 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 heterogeneity was reflected in the absence of viruses shared between Anseriformes and Charadriiformes. Notably, within avian host families there was no significant relationship between either host taxonomy or foraging ecology and virome composition, although Anseriform species positive for influenza A virus harboured more additional viruses than those negative for influenza virus. Overall, we demonstrate complex virome structures across host species that co-exist in multi-species aggregations.

ecology↗