Evidence of reassortment of avian influenza A (H2) viruses in Brazilian shorebirds.

Influenza A viruses of the H2 subtype represent a zoonotic and pandemic threat to humans due to a lack of widespread specific immunity. Although A(H2) viruses that circulate in wild bird reservoirs are distinct from the 1957 pandemic A(H2N2) viruses, there is concern that they could impact animal and public health. There is limited information on AIVs in Latin America, and next to nothing about H2 subtypes in Brazil. In the present study, we report the occurrence and genomic sequences of two influenza A viruses isolated from wild-caught white-rumped sandpipers (Calidris fuscicollis). One virus, identified as A(H2N1), was isolated from a bird captured in Restinga de Jurubatiba National Park (PNRJ, Rio de Janeiro), while the other, identified as A(H2N2), was isolated from a bird captured in Lagoa do Peixe National Park (PNLP, Rio Grande do Sul). DNA sequencing and phylogenetic analysis of the obtained sequences revealed that each virus belonged to distinct subtypes. Furthermore, the phylogenetic analysis indicated that the genomic sequence of the A(H2N1) virus isolated from PNRJ was most closely related to other A(H2N1) viruses isolated from North American birds. On the other hand, the A(H2N2) virus genome recovered from the PNLP-captured bird exhibited a more diverse origin, with some sequences closely related to viruses from Iceland and North America, and others showing similarity to virus sequences recovered from birds in South America. Viral genes of diverse origins were identified in one of the viruses, indicating local reassortment. This suggests that the extreme South of Brazil may serve as an environment conducive to reassortment between avian influenza virus lineages from North and South America, potentially contributing to an increase in overall viral diversity.

Contrasting environmental conditions precluded lower availability of Antarctic krill affecting breeding chinstrap penguins in the Antarctic Peninsula.

Dramatic decreases of chinstrap penguin populations across the Antarctic Peninsula (AP) are thought to be influenced by climate-driven changes affecting its main prey, the Antarctic krill, however, empirical evidence supporting such hypotheses are scarce. By coupling data on breeding chinstrap penguins, environmental remote sensing and estimates of krill acoustic density, we were able to demonstrate that penguins substantially increased their foraging effort in a year of low krill availability, with consequent reduction in breeding success. A winter of low sea ice cover followed by a summer/spring with stronger wind and lower marine productivity explained the lower and deeper krill availability. Our results highlight the importance of environmental variability on penguin populations, as variability is expected to increase under climate change, affecting foraging behaviour responses.

Persistent organic pollutant patterns in seabirds from marine protected areas in the tropical Atlantic Ocean.

Persistent organic pollutants were investigated in the blood of living seabirds (Pterodroma arminjoniana, Onychoprion fuscatus, Sula dactylatra, Anous minutus, Anous stolidus and Sula leucogaster) from two Brazilian Conservation Units - Trindade Island and São Pedro and São Paulo Archipelago. ∑PCBs (0.55 to 55.09 ng/g wet weight (ww), ∑DDTs (0.01 to 17.36 ng/g ww) and Mirex (0.01 to 5.53 ng/g ww) were predominant in all samples. Trindade petrel Pterodroma arminjoniana presented higher values than other seabirds, which is potentially related to diet and migratory behavior. Fluctuations in the trophic ecology data, through carbon and nitrogen stable isotope ratios, warn of temporal variation in diet and foraging and highlight the importance of using a nondestructive matrix to allow long-term monitoring of POP contamination in seabirds from Brazilian Conservation Units. In addition, the data will fill the gaps in the POP baselines for seabirds from the tropical Atlantic Ocean.

H6N8 avian influenza virus in Antarctic seabirds demonstrates connectivity between South America and Antarctica.

Wild aquatic birds are the natural reservoirs of avian influenza viruses (AIVs). It is estimated that 100 million seabirds live in the Antarctic Peninsula and adjacent islands, regularly encountering migratory birds that use the islands to nest. Between 2010 and 2013, we collected samples from 865 seabirds in Elephant, King George and Livingston islands, around Antarctica Peninsula: chinstrap penguin (n = 143); gentoo penguin (n = 208); Adelie penguin (n = 46); brown skua (n = 90); Cape petrel (n = 115) and southern giant petrel (n = 263). Serum (n = 673) samples were analysed by competitive ELISA and swabs (n = 614) were tested by one step real-time RT-PCR for avian influenza virus (AIV). Sera from 30 chinstrap penguins, 76 brown skuas and a single Adelie penguin were seropositive for AIV. Thirteen swab samples were AIV positive by RT-PCR, and complete genome sequences of H6N8 AIVs isolated from brown skua and chinstrap penguin in 2011 were obtained. Phylogenetic analyses indicated that all gene segments of the H6N8 viruses were closely related to Argentinian and Chilean AIVs. The prevalence with which we identified evidence for AIVs infection in various Antarctic seabirds suggest viral circulation in Antarctic avifauna and interspecies viral transmission in the sub-Antarctic region.

Anthropogenic debris in an Antarctic Specially Protected Area in the maritime Antarctic.

Antarctic Specially Protected Areas (ASPAs) provide the strongest environmental protection in Antarctica. However, they are not immune from anthropogenic pollution of marine or terrestrial origin. We document anthropogenic debris within ASPA No. 133 Harmony Point, Nelson Island, recovering 1544 items between November 2019 and January 2020. The majority (82.6 %) were found close to a national operator-constructed refuge and were smaller than 5 cm. Larger items (up to 300 cm) were present on beaches and plateaus. Charcoal and rubber were the most abundant items around the refuge and plastic and metal were the most abundant items on beaches and plateaus. Debris items likely arriving in the area by marine transportation (e.g. plastic) are of concern due to both risk of ingestion and their degradation leading to the release of hazardous chemicals. Such pollution contravenes the terms of the Protocol on Environmental Protection to the Antarctic Treaty and other regionally applicable regulations.

Incidence of anthropogenic material in Sula leucogaster nests in a distant archipelago of Brazil.

Anthropogenic debris has been affecting fauna in different ways. We investigate the frequency of anthropogenic material in nests of a brown booby (Sula leucogaster) colony in the Saint Peter and Saint Paul Archipelago (SPSPA), Rio Grande do Norte, Brazil in February 2015 and November 2016. The items were classified according to type (threadlike plastic, sheet plastics, hard fragments, foamed synthetics and miscellaneous) and color. In 2015, a total of 30 anthropogenic items were found in 20.4% of the nests. In nests containing debris, miscellaneous items were found in 73.6% of nests. White/clear was the most common color, 52.6% of nests containing debris had items of this color. In 2016, 45 anthropogenic items were observed in 13.3% of the nests. Threadlike plastic was found in 59.2% of nests. Blue/purple was the most common color (55.5%). Even far from the Brazilian coast, the S. leucogaster colony has been affected by marine pollution.

Marine debris ingestion and human impacts on the Pygmy sperm whale (Kogia breviceps) in southern Brazil.

Pygmy sperm whales, Kogia breviceps (Kogiidae), are a small cetacean that inhabits Mesopelagic regions near the continental shelf. In this study we present record of plastic ingestion by K. breviceps in Brazil. In August 2010 on the coast of Rio Grande do Sul, a carcass was found showing evidences of interaction with fishing nets. The stomach content was collected for the analysis of food items, but the presence of four plastics weighing 55.9 g was found. In addition, the analysis of food items revealed the presence of the fish Merluccius hubbsi, which is an intensely explored species by fisheries activities in southern Brazil. Merluccius sp. is common in the diet of K. breviceps in several regions of the planet. This work shows that in southern Brazil, K. breviceps suffers intense impact of both ingestion of anthropic material and fisheries, and so must be closely monitored.

Organochlorine pesticides in feathers of three raptor species in southern Brazil.

In this study, we determined the presence of organochlorine pesticides (OCPs) in back feathers from three raptor species, Phalcoboenus chimango, Milvago chimachima and Caracara plancus. Samples were obtained from live animals and ten OCPs were detected: α-HCH, ß-HCH and γ-HCH (lindane), heptachlor, heptachlor epoxide, aldrin, endosulfan I, endosulfan II, endosulfan sulfate and p,p'-DDE. The concentrations found were higher than those reported in other raptor species, and C. plancus showed greater values than P. chimango and M. chimachima for all the substances. These differences may be justified by the species feeding habits and the characteristics of the sampling area, since C. plancus were sampled in an area with a higher concentration of agricultural crops and urbanized environments. In relation to the possible negative effects, four individuals of C. plancus presented DDE values related to sublethal effects for other species. This is the first study reporting OCPs in back feathers of these species in Brazil, and further studies evaluating OCP exposure and related effects are important for a better understanding of the consequences of different OCP concentrations on the health of these species.

More than the eye can see: Genomic insights into the drivers of genetic differentiation in Royal/Macaroni penguins across the Southern Ocean.

The study of systematics in wide-ranging seabirds can be challenging due to the vast geographic scales involved, as well as the possible discordance between molecular, morphological and behavioral data. In the Southern Ocean, macaroni penguins (Eudyptes chrysolophus) are distributed over a circumpolar range including populations in Antarctic and sub-Antarctic areas. Macquarie Island, in its relative isolation, is home to a closely related endemic taxon - the royal penguin (Eudyptes schlegeli), which is distinguishable from E. chrysolophus mainly by facial coloration. Although these sister taxa are widely accepted as representing distinct species based on morphological grounds, the extent of their genome-wide differentiation remains uncertain. In this study, we use genome-wide Single Nucleotide Polymorphisms to test genetic differentiation between these geographically isolated taxa and evaluate the main drivers of population structure among breeding colonies of macaroni/royal penguins. Genetic similarity observed between macaroni and royal penguins suggests they constitute a single evolutionary unit. Nevertheless, royal penguins exhibited a tendency to cluster only with macaroni individuals from Kerguelen Island, suggesting that dispersal occurs mainly between these neighboring colonies. A stepping stone model of differentiation of macaroni/royal populations was further supported by a strong pattern of isolation by distance detected across its whole distribution range, possibly driven by large geographic distances between colonies as well as natal philopatry. However, we also detected intraspecific genomic differentiation between Antarctic and sub-Antarctic populations of macaroni penguins, highlighting the role of environmental factors together with geographic distance in the processes of genetic differentiation between Antarctic and sub-Antarctic waters.

Divergent coronaviruses detected in wild birds in Brazil, including a central park in São Paulo.

Coronaviruses are single-stranded positive-sense RNA viruses associated with important avian diseases. Their relatively high rates of mutation and recombination frequencies allow them to adapt to new hosts and ecological niches. Although Brazil has 18% of global avian species diversity, studies regarding the presence of avian viral diseases in wild birds in South America are scarce. In this study, we performed a retrospective analysis of the presence of CoVs in 746 wild birds. Oropharyngeal and cloacal swabs were obtained and placed together in vials containing VTM transport medium collected in different regions of Brazil between 2006 and 2013. Screening for viral nucleic acid was performed using conventional RT-PCR and pancoronavirus nested PCR. Positive samples were characterized by partial sequencing of the RNA-dependent RNA polymerase (RdRp) gene, and ensuing phylogenetic analysis was performed to investigate the association between virus epidemiology and bird migration routes. Coronavirus RNA were detected and sequenced from six samples, in which three were related to gammacoronaviruses group and the other three to deltacoronavirus group. Our study documents the presence of CoVs related to avian gamma- and deltacoronaviruses circulating in both urban- and poultry-farm regions of Brazil, implicating wild birds as potential carriers of CoVs which may represent a risk to poultry farms and public health in Brazil.

First record of debris ingestion by the shorebird American Oystercatcher (Haematopus palliatus) on the Southern coast of Brazil.

Plastic has become abundant in the oceans and proved to be a threat to marine and coastal fauna. In this study, we present the first record of synthetic debris ingested by the shorebird American Oystercatcher (Haematopus palliatus) in Brazil. We collected 24 stomach contents from October 2007 to October 2015 and 58% were juveniles. Synthetic materials were found in 100% of stomachs. Used plastic fragments and plastic pellets were the most frequent items, beige and white were more common colors. Synthetic material may be unintentionally ingested directly through substrate consumption or indirectly through prey consumption. Hence, debris ingestion may be common, representing an impact to coastal birds. Based on our results, we hope to highlight the need for public policies to reduce the disposal of synthetic debris in the oceans and beaches.

Correction to: Chinstrap penguin population genetic structure: one or more populations along the Southern Ocean?

Correction to: BMC Evolutionary Biology (2018) 18:90 https://doi.org/10.1186/s12862-018-1207-0 .

Chinstrap penguin population genetic structure: one or more populations along the Southern Ocean?

BACKGROUND: Historical factors, demography, reproduction and dispersal are crucial in determining the genetic structure of seabirds. In the Antarctic marine environment, penguins are a major component of the avian biomass, dominant predators and important bioindicators of ecological change. Populations of chinstrap penguins have decreased in nearly all their breeding sites, and their range is expanding throughout the Antarctic Peninsula. Population genetic structure of this species has been studied in some colonies, but not between breeding colonies in the Antarctic Peninsula or at the species' easternmost breeding colony (Bouvetøya). RESULTS: Connectivity, sex-biased dispersal, diversity, genetic structure and demographic history were studied using 12 microsatellite loci and a mitochondrial DNA region (HVRI) in 12 breeding colonies in the South Shetland Islands (SSI) and the Western Antarctic Peninsula (WAP), and one previously unstudied sub-Antarctic island, 3600 km away from the WAP (Bouvetøya). High genetic diversity, evidence of female bias-dispersal and a sign of population expansion after the last glacial maximum around 10,000 mya were detected. Limited population genetic structure and lack of isolation by distance throughout the region were found, along with no differentiation between the WAP and Bouvetøya (overall microsatellite F ST = 0.002, p = 0.273; mtDNA F ST  = - 0.004, p = 0.766), indicating long distance dispersal. Therefore, genetic assignment tests could not assign individuals to their population(s) of origin. The most differentiated location was Georges Point, one of the southernmost breeding colonies of this species in the WAP. CONCLUSIONS: The subtle differentiation found may be explained by some combination of low natal philopatric behavior, high rates of dispersal and/or generally high mobility among colonies of chinstrap penguins compared to other Pygoscelis species.

Migratory birds in southern Brazil are a source of multiple avian influenza virus subtypes.

BACKGROUND: There is insufficient knowledge about the relation of avian influenza virus (AIV) to migratory birds in South America. Accordingly, we studied samples obtained over a 4-year period (2009-2012) from wild birds at a major wintering site in southern Brazil. METHODS: We obtained 1212 oropharyngeal/cloacal samples from wild birds at Lagoa do Peixe National Park and screened them for influenza A virus by RT-PCR amplification of the matrix gene. Virus isolates were subjected to genomic sequencing and antigenic characterization. RESULTS: Forty-eight samples of 1212 (3.96%) contained detectable influenza virus RNA. Partial viral sequences were obtained from 12 of these samples, showing the presence of H2N2 (1), H6Nx (1), H6N1 (8), H9N2 (1), and H12N5 (1) viruses. As H6 viruses predominated, we generated complete genomes from all 9 H6 viruses. Phylogenetic analyses showed that they were most similar to viruses of South American lineage. The H6N1 viruses caused no disease signs in infected ferrets and, despite genetic differences, were antigenically similar to North American isolates. CONCLUSIONS: Lagoa do Peixe National Park is a source of multiple AIV subtypes, with the levels of influenza virus in birds being highest at the end of their wintering period in this region. H6N1 viruses were the predominant subtype identified. These viruses were more similar to viruses of South American lineage than to those of North American lineage.

Novel avian paramyxovirus (APMV-15) isolated from a migratory bird in South America.

A novel avian paramyxovirus (APMV) isolated from a migratory bird cloacal swab obtained during active surveillance in April 2012 in the Lagoa do Peixe National Park, Rio Grande do Sul state, South of Brazil was biologically and genetically characterized. The nucleotide sequence of the full viral genome was completed using a next-generation sequencing approach. The genome was 14,952 nucleotides (nt) long, with six genes (3'-NP-P-M-F-HN-L-5') encoding 7 different proteins, typical of APMV. The fusion (F) protein gene of isolate RS-1177 contained 1,707 nucleotides in a single open reading frame encoding a protein of 569 amino acids. The F protein cleavage site contained two basic amino acids (VPKER↓L), typical of avirulent strains. Phylogenetic analysis of the whole genome indicated that the virus is related to APMV-10, -2 and -8, with 60.1% nucleotide sequence identity to the closest APMV-10 virus, 58.7% and 58.5% identity to the closest APMV-8 and APMV-2 genome, respectively, and less than 52% identity to representatives of the other APMVs groups. Such distances are comparable to the distances observed among other previously identified APMVs serotypes. These results suggest that unclassified/calidris_fuscicollis/Brazil/RS-1177/2012 is the prototype strain of a new APMV serotype, APMV-15.

Vertebrate road kill survey on a highway in southern Brazil / Levantamento de vertebrados atropelados em rodovias do sul do Brasil

Highways are a major factor acting in the decline of several wildlife populations. Impact occurs due to the continuous flow of motor vehicles over tracks and collision with animals using the same area. This study aimed to list road killed wild vertebrates found in highways in the Pampa Biome, state of Rio Grande do Sul, over an entire year. The taxa found (amphibians, reptiles, birds and mammals) were identified to species level and their frequency of occurrence was seasonally registered. Along 2,160 km, we found 318 road killed individuals, totaling 65 species. This number represents an average of 0.147 road killed specimens by kilometer (that is, 1 individual each 7 km). Of these, seven species are under threat of extinction in the state of Rio Grande do Sul. We also found a seasonal pattern among road kills, in which the highest number of road killed animals was registered in the summer and spring months. These results contribute to increase knowledge about which species are most impacted by road kill on highways of the Pampa Biome. Such data can be used as an indicator for the implementation of measures by competent bodies to mitigate impacts of highways in the state of Rio Grande do Sul.

As rodovias são um fator provocador de declínio populacional de diversas espécies da fauna silvestre. O impacto ocorre devido ao contínuo fluxo de veículos automotores sobre as pistas e a colisão dos mesmos com animais que também utilizam essa área. O presente estudo teve por finalidade listar os vertebrados silvestres encontrados atropelados em rodovias no bioma Pampa, no Estado do Rio Grande do Sul, ao longo de um ano. Os táxons encontrados (anfíbios, répteis, aves e mamíferos) foram identificados em nível específico e a sua frequência de ocorrência foi registrada de forma sazonal. Em 2.160 km de estrada percorridos, foram encontrados 318 indivíduos atropelados, totalizando 65 espécies. Essa quantia representa uma média de 0,147 espécimes atropelados por quilômetro (ou seja, 01 indivíduo atropelado a cada 07 Km). Destas, sete espécies estão sob ameaça de extinção no Estado do Rio Grande do Sul. Foram observados padrões sazonais nos atropelamentos, sendo que os meses de verão e da primavera apresentaram o maior número de animais atropelados. Os resultados do estudo contribuem para o conhecimento de quais espécies da fauna silvestre são mais impactadas por atropelamentos no bioma Pampa. Estes dados poderão ser utilizados como orientação na implantação de medidas por órgãos competentes, afim de mitigar o impacto de rodovias no Estado do Rio Grande do Sul.

Marked phylogeographic structure of Gentoo penguin reveals an ongoing diversification process along the Southern Ocean.

Two main hypotheses have been debated about the biogeography of the Southern Ocean: (1) the Antarctic Polar Front (APF), acting as a barrier between Antarctic and sub-Antarctic provinces, and (2) the Antarctic Circumpolar Current (ACC), promoting gene flow among sub-Antarctic areas. The Gentoo penguin is distributed throughout these two provinces, separated by the APF. We analyzed mtDNA (HVR1) and 12 microsatellite loci of 264 Gentoo penguins, Pygoscelis papua, from 12 colonies spanning from the Western Antarctic Peninsula and the South Shetland Islands (WAP) to the sub-Antarctic Islands (SAI). While low genetic structure was detected among WAP colonies (mtDNA ФST=0.037-0.133; microsatellite FST=0.009-0.063), high differentiation was found between all SAI and WAP populations (mtDNA ФST=0.678-0.930; microsatellite FST=0.110-0.290). These results suggest that contemporary dispersal around the Southern Ocean is very limited or absent. As predicted, the APF appears to be a significant biogeographical boundary for Gentoo penguin populations; however, the ACC does not promote connectivity in this species. Our data suggest demographic expansion in the WAP during the last glacial maximum (LGM, about 20kya), but stability in SAI. Phylogenetic analyses showed a deep divergence between populations from the WAP and those from the SAI. Therefore, taxonomy should be further revised. The Crozet Islands resulted as a basal clade (3.57Mya), followed by the Kerguelen Islands (2.32Mya) as well as a more recent divergence between the Falkland/Malvinas Islands and the WAP (1.27Mya). Historical isolation, local adaptation, and past climate scenarios of those Evolutionarily Significant Units may have led to different potentials to respond to climate changes.

Yeasts from macroalgae and lichens that inhabit the South Shetland Islands, Antarctica.

Antarctic terrestrial ecosystems are largely dominated by lichens, while shallow coastal environments are mainly covered by macroalgae. The aim of this study was to isolate and to evaluate the diversity of yeasts in different species of macroalgae and lichens collected in South Shetland Islands, Antarctica. A total of 405 yeasts were recovered (205 from macroalgae and 200 from lichens). The yeast community from macroalgae was most diversity than the yeast community from lichen. The dominance index was similar for both substrates. A total of 24 taxa from macroalgae and 18 from lichens were identified, and only 5 were common to both substrates. Metschnikowia australis, Mrakia sp., Rhodotorula glacialis and Glaciozyma litorale were the most abundant yeasts in macroalgae and Cryptococcus victoriae, Rhodotorula laryngis, Rhodotorula arctica, Trichosporon sp. 1 and Mrakia sp. were the most abundant in lichens. Based on molecular and phylogenetic analyses, four yeast from macroalgae and six from lichens were considered potential new species. This is the first study to report the yeast communities from the Antarctic macroalgae Himantothallus grandifolius and lichen Ramalina terebrata. Results suggest that Antarctic phyco and lichensphere represent a huge substrate for cold-adapted yeasts and enhanced the knowledge of the microbiota from extreme environments.

Southern giant Petrel Macronectes giganteus nest attendance patterns under extreme weather conditions.

Differences in nest attendance between genders in seabirds may be related to morphological differences. Southern giant petrel is a dimorphic species with gender-specific foraging behavior. The objective of this study was to investigate sex-related differences in nest attendance during the breeding period of southern giant petrels by presence/absence patterns of both sexes during incubation and compare use of the colony after nest failure. Fourteen birds were tagged with digitally coded radio-transmitters in a colony at Elephant Island, Antarctica, in the beginning of 2009/2010 breeding season. Females were present during 18 periods (min. 3 days, max. 9 days) and males only in five periods (min. 2 days, max. 13 days). The difference in mean number of radio signals per day between females (4330; s.e. 313.5) and males (2691; s.e. 248.6) was highly significant (t = 4.3; d.f. = 199; P < 0.001; Fig. 4 ). As consequence of the severe weather conditions that year, all tagged birds failed to reproduce. After abandonment of the nests, the presence of both genders decreased drastically, although the tagged individuals stayed in the area. Under severe weather conditions female Southern Giant Petrels continue breeding while males abandon the nest earlier.

Have historical climate changes affected Gentoo penguin (Pygoscelis papua) populations in Antarctica?

The West Antarctic Peninsula (WAP) has been suffering an increase in its atmospheric temperature during the last 50 years, mainly associated with global warming. This increment of temperature trend associated with changes in sea-ice dynamics has an impact on organisms, affecting their phenology, physiology and distribution range. For instance, rapid demographic changes in Pygoscelis penguins have been reported over the last 50 years in WAP, resulting in population expansion of sub-Antarctic Gentoo penguin (P. papua) and retreat of Antarctic Adelie penguin (P. adeliae). Current global warming has been mainly associated with human activities; however these climate trends are framed in a historical context of climate changes, particularly during the Pleistocene, characterized by an alternation between glacial and interglacial periods. During the last maximal glacial (LGM∼21,000 BP) the ice sheet cover reached its maximum extension on the West Antarctic Peninsula (WAP), causing local extinction of Antarctic taxa, migration to lower latitudes and/or survival in glacial refugia. We studied the HRVI of mtDNA and the nuclear intron ßfibint7 of 150 individuals of the WAP to understand the demographic history and population structure of P. papua. We found high genetic diversity, reduced population genetic structure and a signature of population expansion estimated around 13,000 BP, much before the first paleocolony fossil records (∼1,100 BP). Our results suggest that the species may have survived in peri-Antarctic refugia such as South Georgia and North Sandwich islands and recolonized the Antarctic Peninsula and South Shetland Islands after the ice sheet retreat.